| Previous changeset 5:974d8c28e586 (2020-08-17) Next changeset 7:904fb55e9156 (2021-11-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" |
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modified:
macros.xml orthofinder_only_groups.xml |
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| diff -r 974d8c28e586 -r 0ff17c7a18cd macros.xml --- a/macros.xml Mon Aug 17 12:59:19 2020 -0400 +++ b/macros.xml Mon May 03 08:51:01 2021 +0000 |
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| @@ -1,6 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">2.4.0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="citations"> <citations> |
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| diff -r 974d8c28e586 -r 0ff17c7a18cd orthofinder_only_groups.xml --- a/orthofinder_only_groups.xml Mon Aug 17 12:59:19 2020 -0400 +++ b/orthofinder_only_groups.xml Mon May 03 08:51:01 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@"> +<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> @@ -163,7 +163,7 @@ <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> </collection> <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" > - <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']"</filter> + <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> </data> <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" > <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> @@ -199,7 +199,7 @@ </outputs> <tests> <!-- no trees + diamond + input files have no extension fasta/faa/fa --> - <test> + <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="fasta" /> <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" /> @@ -257,7 +257,7 @@ </output> </test> <!-- no trees + diamond + input files have extension fasta/faa/fa --> - <test> + <test expect_num_outputs="6"> <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" /> @@ -315,7 +315,7 @@ </output> </test> <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out --> - <test> + <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" /> @@ -377,7 +377,7 @@ <output_collection name="wdblast" type="list" count="16"/> </test> <!-- no trees + blast + input files have extension fasta/faa/fa--> - <test> + <test expect_num_outputs="6"> <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" /> @@ -436,7 +436,7 @@ </output> </test> <!-- no trees + uploaded blast--> - <test> + <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="blast" /> <param name="input_blast_out"> @@ -482,7 +482,7 @@ <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa --> - <test> + <test expect_num_outputs="9"> <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" /> @@ -540,10 +540,9 @@ </output> <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/> <output_collection name="genetrees" type="list" count="0"/> - <output_collection name="resolved_trees" type="list" count="0"/> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications --> - <test> + <test expect_num_outputs="14"> <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" /> @@ -609,7 +608,7 @@ <output_collection name="resolved_trees" type="list" count="325"/> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> - <test> + <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="fasta" /> <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" /> @@ -672,7 +671,7 @@ </output> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> - <test> + <test expect_num_outputs="9"> <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" /> |