Mercurial > repos > iuc > orthofinder_onlygroups
changeset 7:904fb55e9156 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c"
| author | iuc |
|---|---|
| date | Fri, 19 Nov 2021 10:29:04 +0000 |
| parents | 0ff17c7a18cd |
| children | 3b974afde673 |
| files | macros.xml orthofinder_only_groups.xml |
| diffstat | 2 files changed, 17 insertions(+), 7 deletions(-) [+] |
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--- a/macros.xml Mon May 03 08:51:01 2021 +0000 +++ b/macros.xml Fri Nov 19 10:29:04 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.4.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.5.4</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="citations"> <citations>
--- a/orthofinder_only_groups.xml Mon May 03 08:51:01 2021 +0000 +++ b/orthofinder_only_groups.xml Fri Nov 19 10:29:04 2021 +0000 @@ -1,11 +1,14 @@ <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>finds orthogroups in a set of proteomes</description> + <xrefs> + <xref type="bio.tools">OrthoFinder</xref> + </xrefs> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement> - <requirement type="package" version="2.34">util-linux</requirement> + <requirement type="package" version="2.36">util-linux</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #import re @@ -47,6 +50,7 @@ #if $init.start == "fasta": -f . -S $init.search.search_program + $init.input_type #elif $init.start == "blast": -b . #end if @@ -79,16 +83,21 @@ <inputs> <!-- Control where Orthofinder starts --> <conditional name="init"> - <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run."> - <option value="fasta" selected="true">From fasta proteomes</option> + <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta files' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run."> + <option value="fasta" selected="true">From fasta files</option> <option value="blast">From blast results</option> </param> <when value="fasta"> - <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/> + <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta files" help="One fasta file per species; species and sequence names in the results will remain the same than in the input files."/> + <param name="input_type" type="select" label="Input contains nucleotide or amino acid sequences?"> + <option value="">Amino acid</option> + <option value="-d">Nucleotide</option> + </param> <conditional name="search"> <param name="search_program" type="select" label="Sequence search program"> <option value="diamond" selected="true">Diamond (faster)</option> + <option value="diamond_ultra_sens">Diamond ultra-sensitive</option> <option value="blast">Blast</option> <option value="blast_gz">Blast_gz - blast results gzipped</option> </param> @@ -96,6 +105,7 @@ <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/> </when> <when value="diamond"></when> + <when value="diamond_ultra_sens"></when> <when value="blast_gz"></when> </conditional> </when> @@ -768,7 +778,7 @@ ---------- Parameters ---------- - - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster) + - Sequence search program : You can choose either blast, blast_gz, diamond, or diamond ultra-sensitive (diamond is faster) - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files - Inflation : the inflation parameter; modify this parameter is not recommended.