Mercurial > repos > iuc > orthofinder_onlygroups
changeset 9:b3d25fae5389 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea
| author | iuc |
|---|---|
| date | Mon, 15 Jan 2024 10:18:14 +0000 |
| parents | 3b974afde673 |
| children | |
| files | macros.xml orthofinder_only_groups.xml |
| diffstat | 2 files changed, 47 insertions(+), 9 deletions(-) [+] |
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--- a/macros.xml Sat Nov 27 10:41:07 2021 +0000 +++ b/macros.xml Mon Jan 15 10:18:14 2024 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.5.4</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.5.5</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="citations"> <citations>
--- a/orthofinder_only_groups.xml Sat Nov 27 10:41:07 2021 +0000 +++ b/orthofinder_only_groups.xml Mon Jan 15 10:18:14 2024 +0000 @@ -1,14 +1,13 @@ <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>finds orthogroups in a set of proteomes</description> + <macros> + <import>macros.xml</import> + </macros> <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="2.36">util-linux</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #import re @@ -158,6 +157,9 @@ <!-- Orthogroups results --> <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" /> <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" /> + <data format="tsv" name="hogs" label="OrthoFinder on ${on_string}: hierarchical orthogroups (tsv)" from_work_dir="results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv" > + <filter>trees['run_mode'] == "full"</filter> + </data> <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" /> <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" /> <data format="tsv" name="stat_overall" label="OrthoFinder on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv" /> @@ -492,7 +494,7 @@ <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa --> - <test expect_num_outputs="9"> + <test expect_num_outputs="10"> <conditional name="init"> <param name="start" value="fasta" /> <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" /> @@ -550,9 +552,21 @@ </output> <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/> <output_collection name="genetrees" type="list" count="0"/> + <output name="hogs"> + <assert_contents> + <has_text text="HOG" /> + <has_text text="OG" /> + <has_text text="Gene Tree Parent Clade" /> + <has_text text="Mycoplasma_agalactiae"/> + <has_text text="Mycoplasma_gallisepticum"/> + <has_text text="Mycoplasma_genitalium"/> + <has_text text="Mycoplasma_hyopneumoniae"/> + <has_n_columns n="7"/> + </assert_contents> + </output> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications --> - <test expect_num_outputs="14"> + <test expect_num_outputs="15"> <conditional name="init"> <param name="start" value="fasta" /> <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" /> @@ -616,6 +630,18 @@ <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/> <output_collection name="genetrees" type="list" count="325"/> <output_collection name="resolved_trees" type="list" count="325"/> + <output name="hogs"> + <assert_contents> + <has_text text="HOG" /> + <has_text text="OG" /> + <has_text text="Gene Tree Parent Clade" /> + <has_text text="Mycoplasma_agalactiae"/> + <has_text text="Mycoplasma_gallisepticum"/> + <has_text text="Mycoplasma_genitalium"/> + <has_text text="Mycoplasma_hyopneumoniae"/> + <has_n_columns n="7"/> + </assert_contents> + </output> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> <test expect_num_outputs="6"> @@ -681,7 +707,7 @@ </output> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> - <test expect_num_outputs="9"> + <test expect_num_outputs="10"> <conditional name="init"> <param name="start" value="fasta" /> <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" /> @@ -742,6 +768,18 @@ <has_n_columns n="5"/> </assert_contents> </output> + <output name="hogs"> + <assert_contents> + <has_text text="HOG" /> + <has_text text="OG" /> + <has_text text="Gene Tree Parent Clade" /> + <has_text text="Mycoplasma_agalactiae"/> + <has_text text="Mycoplasma_gallisepticum"/> + <has_text text="Mycoplasma_genitalium"/> + <has_text text="Mycoplasma_hyopneumoniae"/> + <has_n_columns n="7"/> + </assert_contents> + </output> <assert_command> <has_text text="-M 'msa'"/> <has_text text="-A 'muscle'"/>