Mercurial > repos > iuc > mothur_consensus_seqs

comparison consensus.seqs.xml @ 5:e26da66f2ad8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:38:14 -0400
parents 05195067dd2e
children
comparison
equal deleted inserted replaced
4:709e1dd893d3 5:e26da66f2ad8
56 <when value="no"/> 56 <when value="no"/>
57 </conditional> 57 </conditional>
58 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" 58 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base"
59 help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/> 59 help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
60 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/> 60 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/>
61 <expand macro="param-savelog"/>
61 </inputs> 62 </inputs>
62 <outputs> 63 <outputs>
63 <expand macro="logfile-output"/> 64 <expand macro="logfile-output"/>
64 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary"> 65 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary">
65 <filter>perotu['use'] == 'no'</filter> 66 <filter>perotu['use'] == 'no'</filter>
83 <tests> 84 <tests>
84 <test><!-- test with default values --> 85 <test><!-- test with default values -->
85 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 86 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
86 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/> 87 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/>
87 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/> 88 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/>
89 <param name="savelog" value="true"/>
88 <expand macro="logfile-test"/> 90 <expand macro="logfile-test"/>
89 </test> 91 </test>
90 <test><!-- test with list file --> 92 <test><!-- test with list file -->
91 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 93 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
92 <param name="use" value="yes"/> 94 <param name="use" value="yes"/>
100 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/> 102 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/>
101 </output_collection> 103 </output_collection>
102 <output_collection name="consensussummaries" count="3"> 104 <output_collection name="consensussummaries" count="3">
103 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/> 105 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/>
104 </output_collection> 106 </output_collection>
107 <param name="savelog" value="true"/>
105 <expand macro="logfile-test"/> 108 <expand macro="logfile-test"/>
106 </test> 109 </test>
107 </tests> 110 </tests>
108 <help><![CDATA[ 111 <help><![CDATA[
109 112