Mercurial > repos > iuc > mothur_chimera_vsearch
comparison 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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| 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"/> |