Mercurial > repos > iuc > mothur_chimera_vsearch

comparison chimera.vsearch.xml @ 1:b4e60c1d77ac draft

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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
comparison
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0:1801019b4690 1:b4e60c1d77ac
1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1">
2 <description>find potential chimeric sequences using vsearch</description> 2 <description>find potential chimeric sequences using vsearch</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
96 <param argument="mindiffs" type="integer" value="3" min="0" label="minimum number of differences in segment"/> 96 <param argument="mindiffs" type="integer" value="3" min="0" label="minimum number of differences in segment"/>
97 <expand macro="param-savelog"/> 97 <expand macro="param-savelog"/>
98 </inputs> 98 </inputs>
99 <outputs> 99 <outputs>
100 <expand macro="logfile-output"/> 100 <expand macro="logfile-output"/>
101 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/> 101 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
102 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/> 102 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
103 <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
104 <filter>template['source'] == 'self' and template['count']</filter>
105 </data>
103 </outputs> 106 </outputs>
104 <tests> 107 <tests>
105 <test><!-- de novo test with name file --> 108 <test><!-- de novo test with name file -->
106 <param name="fasta" value="stool_small.unique.fasta"/> 109 <param name="fasta" value="stool_small.unique.fasta"/>
107 <param name="source" value="names"/> 110 <param name="source" value="names"/>
110 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/> 113 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
111 <param name="savelog" value="true"/> 114 <param name="savelog" value="true"/>
112 <expand macro="logfile-test"/> 115 <expand macro="logfile-test"/>
113 </test> 116 </test>
114 <test><!-- de novo test with count table--> 117 <test><!-- de novo test with count table-->
115 <param name="fasta" value="stool_small.unique.fasta"/> 118 <param name="fasta" value="chimera.fasta"/>
116 <param name="source" value="self"/> 119 <param name="source" value="self"/>
117 <param name="count" value="stool_small.count_table"/> 120 <param name="count" value="chimera.count_table"/>
118 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/> 121 <param name="dereplicate" value="true"/>
119 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/> 122 <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
123 <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos"/>
124 <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
120 <param name="savelog" value="true"/> 125 <param name="savelog" value="true"/>
121 <expand macro="logfile-test"/> 126 <expand macro="logfile-test"/>
122 </test> 127 </test>
123 <test><!-- test with reference file --> 128 <test><!-- test with reference file -->
124 <param name="fasta" value="stool_small.unique.fasta"/> 129 <param name="fasta" value="stool_small.unique.fasta"/>