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Update orthofinder and pick up new orthogroup output (galaxyproject#5705
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* bump orthofinder

* typo on requirements

* add hog output

* tests
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@TomHarrop
TomHarrop authored Jan 15, 2024
1 parent a1af4fc commit 179e3fd
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Showing 2 changed files with 47 additions and 9 deletions.
4 changes: 2 additions & 2 deletions tools/orthofinder/macros.xml
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<?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>
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52 changes: 45 additions & 7 deletions tools/orthofinder/orthofinder_only_groups.xml
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@@ -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>
<xrefs>
<xref type="bio.tools">OrthoFinder</xref>
</xrefs>
<macros>
<import>macros.xml</import>
</macros>
<xrefs>
<xref type="bio.tools">OrthoFinder</xref>
</xrefs>
<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
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<!-- 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" />
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<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" />
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</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" />
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<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">
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</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" />
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<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'"/>
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