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add galaxy wrappers for methtools
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‎methtools/calling.xml‎

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<tool id="methtools_calling" name="Methylation calling" version="0.1.1">
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<description></description>
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<requirements>
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<requirement type="package" version="0.1_602edc990c6a36e2930f88f3ae5585430164d643">methtools</requirement>
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</requirements>
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<command>
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calling
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--processors 4
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-i $infile
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#if $infile.ext == "bam":
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--bam
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#end if
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#if $cpg == 'true':
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--CpG $cpg_output
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#end if
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#if $chh == 'true':
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--CHH $chh_output
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#end if
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#if $chg == 'true':
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--CHG $chg_output
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#end if
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#if $params.settingsType == "custom":
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$params.phred
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## default 10
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--mincov $params.mincov
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## default 20
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--minqual $params.minqual
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## default 100
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--readlen $params.readlen
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$params.methylkit
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$params.header
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#end if
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</command>
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<inputs>
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<param name="infile" type="data" format="sam,bam" label="SAM or BAM file" help="SAM or BAM file." />
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<param name="cpg" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Calculate CpG methylation scores" help="" />
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<param name="chh" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Calculate CHH methylation scores" help="" />
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<param name="chg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Calculate CHG methylation scores" help="" />
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<conditional name="params">
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<param name="settingsType" type="select" label="Meythylation calling - advanced settings" help="You can use the default settings or set custom values for any parameter.">
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<option value="default">Use Defaults</option>
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<option value="custom">Full parameter list</option>
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</param>
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<when value="default" />
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<!-- Full/advanced params. -->
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<when value="custom">
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<param name="phred" type="boolean" truevalue="--phred64" falsevalue="" checked="False" label="Run FastQC in the default mode on the FastQ file once trimming is complete" help="" />
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<param name="mincov" type="integer" value="10" label="min coverage" help="For more information please see below." />
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<param name="minqual" type="integer" value="20" label="min quality" help="For more information please see below." />
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<param name="readlen" type="integer" value="100" label="Read length" />
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<param name="methylkit" type="boolean" truevalue="--methylkit" falsevalue="" checked="False" label="The generated output files are in methylkit format" help="" />
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<param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Print header line in output files" help="" />
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</when> <!-- full -->
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</conditional> <!-- params -->
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</inputs>
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<outputs>
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<data format="bed" name="cpg_output" label="${tool.name} on ${on_string}: CpG">
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<filter>cpg is True</filter>
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<change_format>
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<when input="params.methylkit" value="--methylkit" format="tabular" />
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</change_format>
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</data>
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<data format="bed" name="chh_output" label="${tool.name} on ${on_string}: CHH">
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<filter>chh is True</filter>
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<change_format>
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<when input="params.methylkit" value="--methylkit" format="tabular" />
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</change_format>
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</data>
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<data format="bed" name="chg_output" label="${tool.name} on ${on_string}: CHG">
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<filter>chg is True</filter>
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<change_format>
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<when input="params.methylkit" value="--methylkit" format="tabular" />
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</change_format>
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</data>
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</outputs>
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<tests>
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</tests>
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<help>
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**What it does**
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Methylation calling of SAM or BAM files produced with bismark. BAM files can be processed in parallel and should be much faster.
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</help>
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</tool>

‎methtools/destrand.xml‎

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<tool id="methtools_destrand" name="destrand" version="0.1.1">
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<description></description>
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<requirements>
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<requirement type="package" version="0.1_602edc990c6a36e2930f88f3ae5585430164d643">methtools</requirement>
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</requirements>
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<command>
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destrand
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-i $infile
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-o $outfile
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</command>
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<inputs>
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<param name="infile" type="data" format="bed" label="BED file." help="" />
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</inputs>
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<outputs>
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<data name="outfile" format="bed" label="${tool.name} on ${on_string}: merged" />
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</outputs>
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<tests>
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</tests>
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<help>
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**What it does**
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Merge CpGs together that are located next to each other. Methylation is symetric, so we can use that trick to enhance the coverage.
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</help>
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</tool>

‎methtools/dmr.xml‎

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<tool id="methtools_dmr" name="Find differentially methylated region (DMR)" version="0.1.1">
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<description></description>
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<requirements>
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<requirement type="package" version="0.1_602edc990c6a36e2930f88f3ae5585430164d643">methtools</requirement>
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</requirements>
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<command>
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dmr
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--control $infile_control
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--affected $infile_affected
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--o $outfile
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$fisher
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#if $min_cov != 0:
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--min-coverage $min_cov
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#end if
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#if $max_cov != 0:
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--max-coverage $max_cov
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#end if
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#if $quantil != 0:
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--filter-quantil $quantil
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#end if
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--min-window-length $min_window_length
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--min-delta-methylation $min_delta_methylation
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--check-last-n $check_last_n
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#if $allow_failed != -1:
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--allow-failed $allow_failed
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#end if
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#if $allow_failed != -1:
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--max-cpg-distance $max_cpg_distance
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#end if
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</command>
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<inputs>
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<param name="infile_control" type="data" format="bed" label="BED file from control sample" help="" />
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<param name="infile_affected" type="data" format="bed" label="BED file from affected sample" help="" />
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<param name="min_cov" type="integer" value="0" label="Minimal allowed coverage" help="0 means no filtering at all" />
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<param name="max_cov" type="integer" value="50" label="Maximal allowed coverage" help="0 means no filtering at all" />
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<param name="quantil" type="float" value="0" label="Filter all site with a greater coverage than the specified quantil (e.g. 0.999)" help="0 means no filtering at all" />
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<param name="fisher" type="boolean" truevalue="--fisher" falsevalue="" checked="False" label="print the fisher-exact-test pvalue for each calculated windoe" help="" />
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<param name="min_window_length" type="integer" value="4" label="minimal window length" />
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<param name="min_delta_methylation" type="integer" value="25" label="minimal delta between the two mehylation states" />
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<param name="check_last_n" type="integer" value="4" label="check last N CpG sites if they fullfill all constraints" />
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<param name="allow_failed" type="integer" value="-1" label="how many sites are allowed to fail in a row" help="-1 means no check at all" />
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<param name="max_cpg_distance" type="integer" value="-1" label="maximal CpG distance" help="-1 means no check at all"/>
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</inputs>
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<outputs>
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<data format="bed" name="outfile" label="${tool.name} on ${on_string}: tiling regions" />
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</outputs>
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<tests>
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</tests>
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<help>
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**What it does**
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Extract differential methylated regions.
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</help>
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</tool>

‎methtools/filter.xml‎

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<tool id="methtools_filter" name="filter BED files" version="0.1.1">
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<description></description>
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<requirements>
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<requirement type="package" version="0.1_602edc990c6a36e2930f88f3ae5585430164d643">methtools</requirement>
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</requirements>
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<command>
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filter
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--control $infile_control
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--affected $infile_affected
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--oaffected $oaffected
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--ocontrol $ocontrol
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#if $pvalue != 0:
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--pvalue $pvalue
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#end if
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#if $min_cov != 0:
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--min-coverage $min_cov
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#end if
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#if $max_cov != 0:
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--max-coverage $max_cov
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#end if
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#if $min_delta_methylation != 0:
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--min-delta-methylation $min_delta_methylation
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#end if
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</command>
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<inputs>
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<param name="infile_control" type="data" format="bed" label="BED file from control sample" help="" />
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<param name="infile_affected" type="data" format="bed" label="BED file from affected sample" help="" />
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<param name="pvalue" type="integer" value="0" label="Fisher Exact Test per methylation site" help="maximal pvalue to classify a site as differential methylated. (0 means no test)" />
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<param name="min_cov" type="integer" value="0" label="Minimal allowed coverage" help="0 means no filtering at all" />
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<param name="max_cov" type="integer" value="0" label="Maximal allowed coverage" help="0 means no filtering at all" />
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<param name="min_delta_methylation" type="integer" value="0" label="minimal delta between the two mehylation states" help="0 means no filtering at all" />
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</inputs>
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<outputs>
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<data format="bed" name="ocontrol" label="${tool.name} on ${on_string}: control" />
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<data format="bed" name="oaffected" label="${tool.name} on ${on_string}: affected" />
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</outputs>
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<tests>
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</tests>
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<help>
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**What it does**
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</help>
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</tool>

‎methtools/plot.xml‎

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<tool id="methtools_plot" name="Plotting" version="0.1.1">
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<description>of methylated regions</description>
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<requirements>
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<requirement type="package" version="0.1_602edc990c6a36e2930f88f3ae5585430164d643">methtools</requirement>
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</requirements>
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<command>
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#import tempfile, os
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#set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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#os.chdir( $temp_dir )
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plot
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--processors 4
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--coordinatefile $coordinatefile
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-i $infile_control $infile_affected
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$overlay_only
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;
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#if $overlay_only == '--overlay-only':
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#cp ./merged.txt $bed_outfile
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#cp ./merged.svg $svg_outfile
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#else:
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#tar -czf $compressed_outfile $temp_dir
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#end if
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##clean tempdir
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#rm $temp_dir -rf
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</command>
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<inputs>
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<param name="infile_control" type="data" format="bed" label="BED file from control sample" help="" />
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<param name="infile_affected" type="data" format="bed" label="BED file from affected sample" help="" />
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<param name="coordinatefile" type="data" format="bed" label="BED file with methylated regions" help="" />
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<param name="overlay_only" type="boolean" truevalue="--overlay-only" falsevalue="" checked="True" label="only create the overlay image" help="" />
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</inputs>
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<outputs>
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<data format="bed" name="bed_outfile" label="${tool.name} on ${on_string}: all plotted regions">
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<filter>overlay_only == "--overlay-only"</filter>
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</data>
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<data format="svg" name="svg_outfile" label="${tool.name} on ${on_string}: overlay image">
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<filter>overlay_only == "--overlay-only"</filter>
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</data>
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<data format="gzipped" name="compressed_outfile" label="${tool.name} on ${on_string}: archive">
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<filter>overlay_only == ""</filter>
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</data>
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</outputs>
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<tests>
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</tests>
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<help>
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**What it does**
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Extract differential methylated regions.
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</help>
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</tool>

‎methtools/tool_dependencies.xml‎

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<?xml version="1.0"?>
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<tool_dependency>
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<package name="methtools" version="0.1_602edc990c6a36e2930f88f3ae5585430164d643">
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<install version="1.0">
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<actions>
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<action type="shell_command">git clone --recursive git://github.com/bgruening/methtools.git</action>
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<action type="shell_command">git checkout 602edc990c6a36e2930f88f3ae5585430164d643</action>
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<action type="shell_command">git submodule update --recursive</action>
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<!--<action type="download_by_url">https://github.com/bgruening/methtools/archive/master.zip</action>-->
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<action type="move_directory_files">
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<source_directory>methtools/</source_directory>
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<destination_directory>$INSTALL_DIR/</destination_directory>
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</action>
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<action type="shell_command">mv $INSTALL_DIR/calling.py $INSTALL_DIR/calling</action>
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<action type="shell_command">mv $INSTALL_DIR/filter.py $INSTALL_DIR/filter</action>
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<action type="shell_command">mv $INSTALL_DIR/destrand.py $INSTALL_DIR/destrand</action>
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<action type="shell_command">mv $INSTALL_DIR/plot.py $INSTALL_DIR/plot</action>
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<action type="shell_command">mv $INSTALL_DIR/dmr.py $INSTALL_DIR/dmr</action>
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<action type="shell_command">chmod +x $INSTALL_DIR/*</action>
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<action type="set_environment">
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<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
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</action>
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</actions>
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</install>
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<readme>
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</readme>
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</package>
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</tool_dependency>
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<!--fisher_exact-->
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