Mercurial > repos > iuc > orthofinder_onlygroups

comparison orthofinder_only_groups.xml @ 6:0ff17c7a18cd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc"
author iuc
date Mon, 03 May 2021 08:51:01 +0000
parents 974d8c28e586
children 904fb55e9156
comparison
equal deleted inserted replaced
5:974d8c28e586 6:0ff17c7a18cd
1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@"> 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> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
161 <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" > 161 <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" >
162 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" /> 162 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" />
163 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> 163 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
164 </collection> 164 </collection>
165 <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" > 165 <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
166 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']"</filter> 166 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
167 </data> 167 </data>
168 <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" > 168 <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
169 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> 169 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
170 </data> 170 </data>
171 171
197 <filter>trees['run_mode'] == "full" and output_duplications</filter> 197 <filter>trees['run_mode'] == "full" and output_duplications</filter>
198 </collection> 198 </collection>
199 </outputs> 199 </outputs>
200 <tests> 200 <tests>
201 <!-- no trees + diamond + input files have no extension fasta/faa/fa --> 201 <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
202 <test> 202 <test expect_num_outputs="6">
203 <conditional name="init"> 203 <conditional name="init">
204 <param name="start" value="fasta" /> 204 <param name="start" value="fasta" />
205 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" /> 205 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
206 <conditional name="search"> 206 <conditional name="search">
207 <param name="search_program" value="diamond"/> 207 <param name="search_program" value="diamond"/>
255 <has_n_columns n="5"/> 255 <has_n_columns n="5"/>
256 </assert_contents> 256 </assert_contents>
257 </output> 257 </output>
258 </test> 258 </test>
259 <!-- no trees + diamond + input files have extension fasta/faa/fa --> 259 <!-- no trees + diamond + input files have extension fasta/faa/fa -->
260 <test> 260 <test expect_num_outputs="6">
261 <conditional name="init"> 261 <conditional name="init">
262 <param name="start" value="fasta" /> 262 <param name="start" value="fasta" />
263 <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" /> 263 <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" />
264 <conditional name="search"> 264 <conditional name="search">
265 <param name="search_program" value="diamond"/> 265 <param name="search_program" value="diamond"/>
313 <has_n_columns n="5"/> 313 <has_n_columns n="5"/>
314 </assert_contents> 314 </assert_contents>
315 </output> 315 </output>
316 </test> 316 </test>
317 <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out --> 317 <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
318 <test> 318 <test expect_num_outputs="10">
319 <conditional name="init"> 319 <conditional name="init">
320 <param name="start" value="fasta" /> 320 <param name="start" value="fasta" />
321 <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" /> 321 <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" />
322 <conditional name="search"> 322 <conditional name="search">
323 <param name="search_program" value="blast"/> 323 <param name="search_program" value="blast"/>
375 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" /> 375 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
376 <output_collection name="wdfasta" type="list" count="4"/> 376 <output_collection name="wdfasta" type="list" count="4"/>
377 <output_collection name="wdblast" type="list" count="16"/> 377 <output_collection name="wdblast" type="list" count="16"/>
378 </test> 378 </test>
379 <!-- no trees + blast + input files have extension fasta/faa/fa--> 379 <!-- no trees + blast + input files have extension fasta/faa/fa-->
380 <test> 380 <test expect_num_outputs="6">
381 <conditional name="init"> 381 <conditional name="init">
382 <param name="start" value="fasta" /> 382 <param name="start" value="fasta" />
383 <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" /> 383 <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" />
384 <conditional name="search"> 384 <conditional name="search">
385 <param name="search_program" value="blast"/> 385 <param name="search_program" value="blast"/>
434 <has_n_columns n="5"/> 434 <has_n_columns n="5"/>
435 </assert_contents> 435 </assert_contents>
436 </output> 436 </output>
437 </test> 437 </test>
438 <!-- no trees + uploaded blast--> 438 <!-- no trees + uploaded blast-->
439 <test> 439 <test expect_num_outputs="6">
440 <conditional name="init"> 440 <conditional name="init">
441 <param name="start" value="blast" /> 441 <param name="start" value="blast" />
442 <param name="input_blast_out"> 442 <param name="input_blast_out">
443 <collection type="list"> 443 <collection type="list">
444 <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/> 444 <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/>
480 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/> 480 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
481 <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/> 481 <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
482 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/> 482 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
483 </test> 483 </test>
484 <!-- full mode + diamond + input files have extension fasta/faa/fa --> 484 <!-- full mode + diamond + input files have extension fasta/faa/fa -->
485 <test> 485 <test expect_num_outputs="9">
486 <conditional name="init"> 486 <conditional name="init">
487 <param name="start" value="fasta" /> 487 <param name="start" value="fasta" />
488 <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" /> 488 <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" />
489 <conditional name="search"> 489 <conditional name="search">
490 <param name="search_program" value="diamond"/> 490 <param name="search_program" value="diamond"/>
538 <has_n_columns n="5"/> 538 <has_n_columns n="5"/>
539 </assert_contents> 539 </assert_contents>
540 </output> 540 </output>
541 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/> 541 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
542 <output_collection name="genetrees" type="list" count="0"/> 542 <output_collection name="genetrees" type="list" count="0"/>
543 <output_collection name="resolved_trees" type="list" count="0"/>
544 </test> 543 </test>
545 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications --> 544 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
546 <test> 545 <test expect_num_outputs="14">
547 <conditional name="init"> 546 <conditional name="init">
548 <param name="start" value="fasta" /> 547 <param name="start" value="fasta" />
549 <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" /> 548 <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 <conditional name="search"> 549 <conditional name="search">
551 <param name="search_program" value="diamond"/> 550 <param name="search_program" value="diamond"/>
607 <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/> 606 <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
608 <output_collection name="genetrees" type="list" count="325"/> 607 <output_collection name="genetrees" type="list" count="325"/>
609 <output_collection name="resolved_trees" type="list" count="325"/> 608 <output_collection name="resolved_trees" type="list" count="325"/>
610 </test> 609 </test>
611 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> 610 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
612 <test> 611 <test expect_num_outputs="6">
613 <conditional name="init"> 612 <conditional name="init">
614 <param name="start" value="fasta" /> 613 <param name="start" value="fasta" />
615 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" /> 614 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
616 <conditional name="search"> 615 <conditional name="search">
617 <param name="search_program" value="diamond"/> 616 <param name="search_program" value="diamond"/>
670 <has_n_columns n="5"/> 669 <has_n_columns n="5"/>
671 </assert_contents> 670 </assert_contents>
672 </output> 671 </output>
673 </test> 672 </test>
674 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> 673 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
675 <test> 674 <test expect_num_outputs="9">
676 <conditional name="init"> 675 <conditional name="init">
677 <param name="start" value="fasta" /> 676 <param name="start" value="fasta" />
678 <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" /> 677 <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" />
679 <conditional name="search"> 678 <conditional name="search">
680 <param name="search_program" value="diamond"/> 679 <param name="search_program" value="diamond"/>