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mvdbeekmvdbeek
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Retab more fastx tools
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-76
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7 files changed

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‎tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml

+46-46
Original file line numberDiff line numberDiff line change
@@ -1,54 +1,54 @@
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<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="@VERSION@">
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<description>converter from FASTX-toolkit</description>
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<description>converter from FASTX-toolkit</description>
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<expand macro="requirements" />
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<macros>
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<import>fastx_macros.xml</import>
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</macros>
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<command>
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<![CDATA[
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gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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<inputs>
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<param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
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<param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
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<option value="">yes</option>
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<option value="-n">no</option>
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</param>
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<param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
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<option value="-r">yes</option>
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<option value="">no</option>
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</param>
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</inputs>
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<tests>
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<test>
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<!-- FASTQ-To-FASTA, keep N, don't rename -->
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<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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<param name="SKIPN" value=""/>
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<param name="RENAMESEQ" value=""/>
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<output name="output" file="fastq_to_fasta1a.out" />
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</test>
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<test>
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<!-- FASTQ-To-FASTA, discard N, rename -->
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<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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<param name="SKIPN" value="no"/>
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<param name="RENAMESEQ" value="yes"/>
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<output name="output" file="fastq_to_fasta1b.out" />
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</test>
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</tests>
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<outputs>
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<data format="fasta" name="output" metadata_source="input" />
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</outputs>
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<command>
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<![CDATA[
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gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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<inputs>
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<param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
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<param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
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<option value="">yes</option>
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<option value="-n">no</option>
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</param>
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<param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
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<option value="-r">yes</option>
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<option value="">no</option>
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</param>
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</inputs>
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<tests>
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<test>
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<!-- FASTQ-To-FASTA, keep N, don't rename -->
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<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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<param name="SKIPN" value=""/>
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<param name="RENAMESEQ" value=""/>
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<output name="output" file="fastq_to_fasta1a.out" />
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</test>
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<test>
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<!-- FASTQ-To-FASTA, discard N, rename -->
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<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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<param name="SKIPN" value="no"/>
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<param name="RENAMESEQ" value="yes"/>
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<output name="output" file="fastq_to_fasta1b.out" />
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</test>
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</tests>
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<outputs>
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<data format="fasta" name="output" metadata_source="input" />
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</outputs>
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<help>
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‎tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml

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@@ -7,11 +7,11 @@
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<command>
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<![CDATA[
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zcat -f < '$input' | fastx_clipper -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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‎tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml

+5-5
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<command>
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<![CDATA[
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zcat -f < '$input' | fastx_collapser -v -o '$output'
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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‎tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml

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<command>
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<![CDATA[
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zcat -f < '$input' | fastx_quality_stats -o '$output'
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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‎tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml

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<command>
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<![CDATA[
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zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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‎tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml

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@@ -7,11 +7,11 @@
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<command>
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<![CDATA[
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zcat -f < '$input' | fastx_reverse_complement -v -o '$output'
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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<inputs>

‎tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml

+5-5
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<command>
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<![CDATA[
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zcat -f < '$input' | fastx_trimmer -v -f $first -l $last -o '$output'
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
14-
#end if
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#if $input.ext == "fastqsanger":
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-Q 33
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#elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
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-Q 64
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#end if
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]]>
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</command>
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