added orthologer tool #7604
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| name: orthologer | ||
| owner: iuc | ||
| description: Ortholog detection. | ||
| long_description: Ortholog detection for comparative genomics and fast functional annotation behind OrthoDB and BUSCO. | ||
| categories: | ||
| - Sequence Analysis | ||
| - Phylogenetics | ||
| homepage_url: https://orthologer.ezlab.org | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthologer | ||
| type: unrestricted |
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| <tool id="ODB-mapper" name="Map to orthology" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>Map FASTA to OrthoDB orthology</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <expand macro="version_command"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ## set the number of threads to be used | ||
| export NTHREADS=\${GALAXY_SLOTS:-1} && | ||
| ODB-mapper SETUP && | ||
| ODB-mapper MAP odbmap | ||
| odbmap:'$fasta' | ||
| #if '$node': | ||
| '$node' | ||
| #end if | ||
| ## | ||
| ## softlink result files - the directory name depends on OrthoDB version used in the mapping | ||
| && results_path="\$(ODB-mapper CONFIG project)/Results" | ||
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Member
There was a problem hiding this comment. Out of interest where is this safed? Can we not provide this path upfront?
Author
There was a problem hiding this comment. As in a previous comment, the path depends on the OrthoDB API version used. In principle the mapper can be run on different OrthoDB versions although I have not implemented it here.
Author
There was a problem hiding this comment. In principle the whole result path could be interesting. In a galaxy context, how can one provide a whole path with its content?
Member
There was a problem hiding this comment. You can use PWD/CWD and put the results in ./results.
Contributor
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You mean that you want to provide it as an output? For this the |
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| && grep -v '^#' \$results_path/odbmap.og.annotations > odbmap.og.annotations | ||
| && grep -v '^#' \$results_path/odbmap.og.odb > odbmap.og.odb | ||
| && grep -v '^#' \$results_path/odbmap.og.hits | awk '{print$1,$2}' | sort > odbmap.og.hits | ||
| && ln -sf \$results_path/odbmap.summary.txt ./ | ||
| ]]></command> | ||
| <inputs> | ||
| <param type="data" name="fasta" format="fasta" label="Input FASTA file"/> | ||
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| <param type="integer" name="node" optional="true" label="optional OrthDB node as NCBI taxid - if not given, it uses busco autolineage to establish node"/> | ||
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| </inputs> | ||
| <outputs> | ||
| <data name="annotations" label="${tool.name} on ${on_string} : mapped genes with annotations" format="tsv" from_work_dir="odbmap.og.annotations"> | ||
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| <actions> | ||
| <action name="column_names" type="metadata" default="query,odb_og,evalue,score,COG_category,Description,GOs_mf,GOs_bp,EC,KEGG_ko,Interpro" /> | ||
| </actions> | ||
| </data> | ||
| <data name="clusters" label="${tool.name} on ${on_string} : clusters with OrthoDB ids" format="txt" from_work_dir="odbmap.og.odb"> | ||
| <actions> | ||
| <action name="column_names" type="metadata" default="odb_og,gene_id,og_type,nvertices,ali_start,ali_end,pid,score,evalue" /> | ||
| </actions> | ||
| </data> | ||
| <data name="hits" label="${tool.name} on ${on_string} : mapped genes and OrthoDB cluster ids" format="txt" from_work_dir="odbmap.og.hits"> | ||
| <actions> | ||
| <action name="column_names" type="metadata" default="odb_og,gene_id" /> | ||
| </actions> | ||
| </data> | ||
| <data name="summary" label="${tool.name} on ${on_string} : clustering stats" format="txt" from_work_dir="odbmap.summary.txt" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="4"> | ||
| <param name="fasta" value="example.fs"/> | ||
| <param name="node" value="1489911"/> | ||
| <output name="hits" file="refhits.og" lines_diff="2"/> | ||
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| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
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| This tool maps a given fasta file against OrthoDB orthology. | ||
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Contributor
There was a problem hiding this comment. Does this query online data? How much data is transferred?
Author
There was a problem hiding this comment. Yes this downloads data and it may vary a lot depending on which target level is chosen.
Contributor
There was a problem hiding this comment. I think we should cache the orthodb locally. Potentially downloading GB per job seems not to be a good idea if it can be avoided. Seems that
Author
There was a problem hiding this comment. Ok, yes that is true - not sure how to set it in a galaxy environment though.
Contributor
There was a problem hiding this comment. Some docs are here: https://docs.galaxyproject.org/en/master/admin/data_tables.html https://docs.galaxyproject.org/en/master/dev/data_managers.html Maybe the busco data table gives a bit of inspiration... |
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| The level is given as an NCBI taxid (e.g 33208 for Metazoa). | ||
| If no level is given, a level is selected using busco autolineage. | ||
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| Taxids can be found at `NCBI <https://www.ncbi.nlm.nih.gov/taxonomy>`_ . | ||
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| For more information | ||
| * `orthologer user manual <https://orthologer.ezlab.org>`_ | ||
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| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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| <macros> | ||
| <token name="@TOOL_VERSION@">3.9.0</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">25.0</token> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1093/nar/gkae987</citation> | ||
| </citations> | ||
| </xml> | ||
| <xml name="version_command"> | ||
| <version_command><![CDATA[ODB-mapper CONFIG]]></version_command> | ||
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| </xml> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">orthologer</requirement> | ||
| </requirements> | ||
| </xml> | ||
| </macros> | ||
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Shhoudb't name and id be orthologer?
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Sorry I had missed this comment! True, the orthologer package contains two main tools.
One that computes orthology from a set of fasta files. The other one is based on that one but maps a given fasta file to OrthoDB data. The priority was to first add the mapper tool. My intention is to add the orthologer tool as well.
Maybe another naming scheme would be appropriate?
Thinking about it a bit more - computing orthology is usually done over many fasta files. That's not very suitable in this environment. It will quickly use a lot of resources.
I noticed that FastOMA gives a warning about that particular issue.
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In this case we should add
suiteandauto_tool_repositoriesto the.shed.yamlfile, see eg https://github.com/galaxyproject/tools-iuc/blob/main/tools/ampvis2/.shed.ymlHow about
name="orthologer map"and<description>FASTA to OrthoDB orthology</description>. This would render asorthologer map: FASTA to OrthoDB orthology.There was a problem hiding this comment.
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Indeed in the current setup a separate job would be created for each input fasta. Which gives maximum possible parallelisation (but overhead of job creation). What is the processing time per fasta? An alternative would be to use
multiple="true"in the fasta input. Then a single job would be created and the loop over the files needs to be done in the tool command (The user may still create appropriately sized jobs by using collections --- but this is then for advanced users).Not sure if the fastoma comment applies to your tool (xref. The reasoning there was that the tool wraps a whole workflow instead of implementing the workflow in Galaxy - which limits achievable parallelisation.
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To summarize, the two modes in orthologer are quite different:
Your suggestion of allowing multiple fasta files to ODB-mapper makes sense. I will do that.
I'm working on the second to test locally but would prefer to publish that one later.
Your suggestion for names also makes sense. I will make the changes.
I will also update the .shed.yml according to your suggestion in order to prepare for including the 2nd tool.