Mercurial > repos > iuc > mothur_chimera_vsearch
diff chimera.vsearch.xml @ 1:b4e60c1d77ac draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author | iuc |
---|---|
date | Fri, 06 Apr 2018 04:13:19 -0400 |
parents | 1801019b4690 |
children | de3cfb122105 |
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--- a/chimera.vsearch.xml Tue Mar 20 22:09:26 2018 -0400 +++ b/chimera.vsearch.xml Fri Apr 06 04:13:19 2018 -0400 @@ -1,4 +1,4 @@ -<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.0"> +<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1"> <description>find potential chimeric sequences using vsearch</description> <macros> <import>macros.xml</import> @@ -98,8 +98,11 @@ </inputs> <outputs> <expand macro="logfile-output"/> - <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/> - <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/> + <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${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> + </data> </outputs> <tests> <test><!-- de novo test with name file --> @@ -112,11 +115,13 @@ <expand macro="logfile-test"/> </test> <test><!-- de novo test with count table--> - <param name="fasta" value="stool_small.unique.fasta"/> + <param name="fasta" value="chimera.fasta"/> <param name="source" value="self"/> - <param name="count" value="stool_small.count_table"/> - <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/> - <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/> + <param name="count" value="chimera.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_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test>