Mercurial > repos > iuc > mothur_chimera_vsearch
diff chimera.vsearch.xml @ 7:de3cfb122105 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author | iuc |
---|---|
date | Fri, 22 Jan 2021 01:09:52 +0000 |
parents | b4e60c1d77ac |
children | bdb4a58a2025 |
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--- a/chimera.vsearch.xml Tue Dec 08 14:17:28 2020 +0000 +++ b/chimera.vsearch.xml Fri Jan 22 01:09:52 2021 +0000 @@ -1,4 +1,4 @@ -<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1"> +<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.2"> <description>find potential chimeric sequences using vsearch</description> <macros> <import>macros.xml</import> @@ -101,11 +101,11 @@ <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/> <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/> <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table"> - <filter>template['source'] == 'self' and template['count']</filter> + <filter>template['source'] == 'self' and template['count'] and template['count'].metadata.groups != []</filter> </data> </outputs> <tests> - <test><!-- de novo test with name file --> + <test expect_num_outputs="3"><!-- de novo test with name file --> <param name="fasta" value="stool_small.unique.fasta"/> <param name="source" value="names"/> <param name="name" value="stool_small.names"/> @@ -114,18 +114,29 @@ <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> - <test><!-- de novo test with count table--> + <test expect_num_outputs="4"><!-- de novo test with count table--> <param name="fasta" value="chimera.fasta"/> <param name="source" value="self"/> - <param name="count" value="chimera.count_table"/> + <param name="count" value="chimera.count_table" ftype="mothur.count_table"/> <param name="dereplicate" value="true"/> <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/> - <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos"/> + <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/> <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> - <test><!-- test with reference file --> + <test expect_num_outputs="3"><!-- de novo test with count table (missing group info)--> + <param name="fasta" value="chimera.fasta"/> + <param name="source" value="self"/> + <param name="count" value="chimera.count_table_wogroups" ftype="mothur.count_table"/> + <param name="dereplicate" value="true"/> + <!-- for some reason only for count tables wo group info header is printed --> + <output name="vsearch.chimeras" file="chimera.vsearch.chimeras_wogroups" ftype="txt"/> + <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/> + <param name="savelog" value="true"/> + <expand macro="logfile-test"/> + </test> + <test expect_num_outputs="3"><!-- test with reference file --> <param name="fasta" value="stool_small.unique.fasta"/> <param name="source" value="hist"/> <param name="reference" value="stool_small.unique.fasta"/>