Mercurial > repos > iuc > orthofinder_onlygroups

comparison orthofinder_only_groups.xml @ 9:b3d25fae5389 draft default tip

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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
comparison
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8:3b974afde673 9:b3d25fae5389
1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>finds orthogroups in a set of proteomes</description> 2 <description>finds orthogroups in a set of proteomes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">OrthoFinder</xref> 7 <xref type="bio.tools">OrthoFinder</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
11 <requirement type="package" version="2.36">util-linux</requirement>
12 </requirements> 11 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
14 #import re 13 #import re
15 ## prepare inputs 14 ## prepare inputs
16 #if $init.start == "fasta": 15 #if $init.start == "fasta":
156 </inputs> 155 </inputs>
157 <outputs> 156 <outputs>
158 <!-- Orthogroups results --> 157 <!-- Orthogroups results -->
159 <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" /> 158 <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" />
160 <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" /> 159 <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" />
160 <data format="tsv" name="hogs" label="OrthoFinder on ${on_string}: hierarchical orthogroups (tsv)" from_work_dir="results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv" >
161 <filter>trees['run_mode'] == "full"</filter>
162 </data>
161 <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" /> 163 <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" />
162 <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" /> 164 <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" />
163 <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" /> 165 <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" />
164 <data format="tsv" name="stat_specs" label="OrthoFinder on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv" /> 166 <data format="tsv" name="stat_specs" label="OrthoFinder on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv" />
165 167
490 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/> 492 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
491 <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/> 493 <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
492 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/> 494 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
493 </test> 495 </test>
494 <!-- full mode + diamond + input files have extension fasta/faa/fa --> 496 <!-- full mode + diamond + input files have extension fasta/faa/fa -->
495 <test expect_num_outputs="9"> 497 <test expect_num_outputs="10">
496 <conditional name="init"> 498 <conditional name="init">
497 <param name="start" value="fasta" /> 499 <param name="start" value="fasta" />
498 <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" /> 500 <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" />
499 <conditional name="search"> 501 <conditional name="search">
500 <param name="search_program" value="diamond"/> 502 <param name="search_program" value="diamond"/>
548 <has_n_columns n="5"/> 550 <has_n_columns n="5"/>
549 </assert_contents> 551 </assert_contents>
550 </output> 552 </output>
551 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/> 553 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
552 <output_collection name="genetrees" type="list" count="0"/> 554 <output_collection name="genetrees" type="list" count="0"/>
555 <output name="hogs">
556 <assert_contents>
557 <has_text text="HOG" />
558 <has_text text="OG" />
559 <has_text text="Gene Tree Parent Clade" />
560 <has_text text="Mycoplasma_agalactiae"/>
561 <has_text text="Mycoplasma_gallisepticum"/>
562 <has_text text="Mycoplasma_genitalium"/>
563 <has_text text="Mycoplasma_hyopneumoniae"/>
564 <has_n_columns n="7"/>
565 </assert_contents>
566 </output>
553 </test> 567 </test>
554 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications --> 568 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
555 <test expect_num_outputs="14"> 569 <test expect_num_outputs="15">
556 <conditional name="init"> 570 <conditional name="init">
557 <param name="start" value="fasta" /> 571 <param name="start" value="fasta" />
558 <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" /> 572 <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" />
559 <conditional name="search"> 573 <conditional name="search">
560 <param name="search_program" value="diamond"/> 574 <param name="search_program" value="diamond"/>
614 <output name="duplications" value="results/Duplications.tsv" compare="sim_size"/> 628 <output name="duplications" value="results/Duplications.tsv" compare="sim_size"/>
615 <output name="duplications_per_orthogroup" value="results/Duplications_per_Orthogroup.tsv" compare="sim_size"/> 629 <output name="duplications_per_orthogroup" value="results/Duplications_per_Orthogroup.tsv" compare="sim_size"/>
616 <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/> 630 <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
617 <output_collection name="genetrees" type="list" count="325"/> 631 <output_collection name="genetrees" type="list" count="325"/>
618 <output_collection name="resolved_trees" type="list" count="325"/> 632 <output_collection name="resolved_trees" type="list" count="325"/>
633 <output name="hogs">
634 <assert_contents>
635 <has_text text="HOG" />
636 <has_text text="OG" />
637 <has_text text="Gene Tree Parent Clade" />
638 <has_text text="Mycoplasma_agalactiae"/>
639 <has_text text="Mycoplasma_gallisepticum"/>
640 <has_text text="Mycoplasma_genitalium"/>
641 <has_text text="Mycoplasma_hyopneumoniae"/>
642 <has_n_columns n="7"/>
643 </assert_contents>
644 </output>
619 </test> 645 </test>
620 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> 646 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
621 <test expect_num_outputs="6"> 647 <test expect_num_outputs="6">
622 <conditional name="init"> 648 <conditional name="init">
623 <param name="start" value="fasta" /> 649 <param name="start" value="fasta" />
679 <has_n_columns n="5"/> 705 <has_n_columns n="5"/>
680 </assert_contents> 706 </assert_contents>
681 </output> 707 </output>
682 </test> 708 </test>
683 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> 709 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
684 <test expect_num_outputs="9"> 710 <test expect_num_outputs="10">
685 <conditional name="init"> 711 <conditional name="init">
686 <param name="start" value="fasta" /> 712 <param name="start" value="fasta" />
687 <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" /> 713 <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" />
688 <conditional name="search"> 714 <conditional name="search">
689 <param name="search_program" value="diamond"/> 715 <param name="search_program" value="diamond"/>
738 <has_text text="Number of genes per-species in orthogroup"/> 764 <has_text text="Number of genes per-species in orthogroup"/>
739 <has_text text="Percentage of orthogroups"/> 765 <has_text text="Percentage of orthogroups"/>
740 <has_text text="Number of orthogroups"/> 766 <has_text text="Number of orthogroups"/>
741 <has_text text="Number of genes"/> 767 <has_text text="Number of genes"/>
742 <has_n_columns n="5"/> 768 <has_n_columns n="5"/>
769 </assert_contents>
770 </output>
771 <output name="hogs">
772 <assert_contents>
773 <has_text text="HOG" />
774 <has_text text="OG" />
775 <has_text text="Gene Tree Parent Clade" />
776 <has_text text="Mycoplasma_agalactiae"/>
777 <has_text text="Mycoplasma_gallisepticum"/>
778 <has_text text="Mycoplasma_genitalium"/>
779 <has_text text="Mycoplasma_hyopneumoniae"/>
780 <has_n_columns n="7"/>
743 </assert_contents> 781 </assert_contents>
744 </output> 782 </output>
745 <assert_command> 783 <assert_command>
746 <has_text text="-M 'msa'"/> 784 <has_text text="-M 'msa'"/>
747 <has_text text="-A 'muscle'"/> 785 <has_text text="-A 'muscle'"/>