| Previous changeset 1:918d141a166b (2017-12-03) Next changeset 3:1aed170afb2b (2019-12-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 |
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modified:
orthofinder_only_groups.xml |
| b |
| diff -r 918d141a166b -r 649b98adce77 orthofinder_only_groups.xml --- a/orthofinder_only_groups.xml Sun Dec 03 04:30:59 2017 -0500 +++ b/orthofinder_only_groups.xml Tue Mar 06 11:10:03 2018 -0500 |
| [ |
| b'@@ -1,26 +1,26 @@\n-<tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">\n+<tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="2.1.2">\n <description>finds orthogroups in a set of proteomes</description>\n <requirements>\n- <requirement type="package" version="1.1.4">orthofinder</requirement>\n+ <requirement type="package" version="2.1.2">orthofinder</requirement>\n </requirements>\n <command>\n <![CDATA[\n ## prepare inputs\n- #if $init.start=="fasta":\n+ #if $init.start == "fasta":\n #set $infiles = ""\n #for $input in $init.input_fasta\n ln -s \'$input\' \'${input.element_identifier}.fasta\' &&\n #set $infiles = $infiles + str($input.element_identifier) + ","\n #end for\n #set $infiles = $infiles[:-1]\n- #elif $init.start=="blast":\n+ #elif $init.start == "blast":\n #set $infilesbl = ""\n #for $input in $init.input_blast_out\n ln -s \'$input\' \'$input.element_identifier\' &&\n #set $infilesbl = $infilesbl + str($input.element_identifier) + ","\n #end for\n #set $infilesbl = $infilesbl[:-1]\n- \n+\n #set $infilesfa = ""\n #for $input in $init.input_blast_fa\n ln -s \'$input\' \'$input.element_identifier\' &&\n@@ -34,28 +34,30 @@\n \n ## start Orthofinder\n orthofinder\n- #if $init.start=="fasta":\n+ #if $init.start == "fasta":\n -f .\n- #elif $init.start=="blast":\n+ -S $init.search.search_program\n+ #elif $init.start == "blast":\n -b .\n #end if\n \n -I $I -og -t \\${GALAXY_SLOTS:-1} -a \\${GALAXY_SLOTS:-1} &&\n \n- #if $init.start=="fasta":\n+ #if $init.start == "fasta":\n mv Results_* results\n- #if $init.keepblastout=="yes":\n- && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&\n- mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&\n- mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/\n+ #if $init.search.search_program == "blast":\n+ #if $init.search.keepblastout:\n+ && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&\n+ mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&\n+ mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/\n+ #end if\n #end if\n- #elif $init.start=="blast":\n+ #elif $init.start == "blast":\n mkdir results &&\n mv *.csv results/ &&\n mv Orthogroups.txt results/\n #end if\n- \n- ]]> \n+ ]]>\n </command>\n <inputs>\n <!-- Control where Orthofinder starts -->\n@@ -67,7 +69,18 @@\n \n <when value="fasta">\n <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."/>\n- <param name="keepblastout" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Do you want to get the blast results ?" help="Used to re-run OrthoFinder_OnlyGroups from pre-computed blast results"/> \n+ <conditional name="search">\n+ <param name="search_program" type="select" label="Sequence search program" help="Choose between blast, blast_gz, diamond">\n+ <option value="blast" selected="true">blast</option>\n+ <option value="blast_gz">blast_gz</option>\n+ <option value="diamond">diamond</option>\n+ </param>\n+ <when value="blast">\n+ <param name="keepblas'..b'="search_program" value="blast"/>\n+ <param name="keepblastout" value="true" />\n+ </conditional>\n </conditional>\n <param name="inflation" value="1.5" />\n <output name="specs_overlap">\n@@ -268,7 +293,63 @@\n <output_collection name="wdfasta" type="list" count="4"/>\n <output_collection name="wdblast" type="list" count="16"/>\n </test>\n- \n+\n+ <!-- test -S diamond -->\n+ <test>\n+ <conditional name="init">\n+ <param name="start" value="fasta" />\n+ <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />\n+ <conditional name="search">\n+ <param name="search_program" value="diamond"/>\n+ </conditional>\n+ </conditional>\n+ <param name="inflation" value="1.5" />\n+ <output name="specs_overlap">\n+ <assert_contents>\n+ <has_text text="Mycoplasma_agalactiae"/>\n+ <has_text text="Mycoplasma_gallisepticum"/>\n+ <has_text text="Mycoplasma_genitalium"/>\n+ <has_text text="Mycoplasma_hyopneumoniae"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="unassigned_genes">\n+ <assert_contents>\n+ <has_text text="Mycoplasma_agalactiae"/>\n+ <has_text text="Mycoplasma_gallisepticum"/>\n+ <has_text text="Mycoplasma_genitalium"/>\n+ <has_text text="Mycoplasma_hyopneumoniae"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="stat_overall">\n+ <assert_contents>\n+ <has_text text="Number of genes in orthogroups"/>\n+ <has_text text="Number of unassigned genes"/>\n+ <has_text text="Percentage of orthogroups"/>\n+ <has_text text="Number of orthogroups"/>\n+ <has_text text="Number of genes"/>\n+ <has_text text="G50 (assigned genes)"/>\n+ <has_text text="G50 (all genes)"/>\n+ <has_text text="O50 (assigned genes)"/>\n+ <has_text text="O50 (all genes)"/>\n+ </assert_contents>\n+ </output>\n+ <output name="stat_specs">\n+ <assert_contents>\n+ <has_text text="Mycoplasma_agalactiae"/>\n+ <has_text text="Mycoplasma_gallisepticum"/>\n+ <has_text text="Mycoplasma_genitalium"/>\n+ <has_text text="Mycoplasma_hyopneumoniae"/>\n+ <has_text text="Number of genes per-species in orthogroup"/>\n+ <has_text text="Percentage of orthogroups"/>\n+ <has_text text="Number of orthogroups"/>\n+ <has_text text="Number of genes"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n <!-- test orthofinder -b -og -->\n <test>\n <conditional name="init">\n@@ -339,6 +420,13 @@\n - The SpeciesIDs.txt file\n - The SequencesIDs.txt file\n \n+----------\n+Parameters\n+----------\n+ - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster)\n+ - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files\n+ - Inflation : the inflation parameter; modify this parameter is not recommended.\n+\n </help>\n <citations>\n <citation type="doi">10.1186/s13059-015-0721-2</citation>\n' |