Mercurial > repos > iuc > mothur_chimera_ccode

comparison chimera.ccode.xml @ 5:8fd55f09d7e8 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 13:47:34 -0400
parents d3f6d99d7ad7
children fd378a7b7c99
comparison
equal deleted inserted replaced
4:bf06e2c30438 5:8fd55f09d7e8
68 </conditional> 68 </conditional>
69 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed" 69 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed"
70 help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length. Default is used if &lt; 1"/> 70 help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length. Default is used if &lt; 1"/>
71 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query" 71 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query"
72 help="uses default if set to 0"/> 72 help="uses default if set to 0"/>
73 <expand macro="param-savelog"/>
73 </inputs> 74 </inputs>
74 <outputs> 75 <outputs>
75 <expand macro="logfile-output"/> 76 <expand macro="logfile-output"/>
76 <data name="ccode.chimeras" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/> 77 <data name="ccode.chimeras" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
77 <data name="ccode.accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/> 78 <data name="ccode.accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
87 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/> 88 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
88 </assert_contents> 89 </assert_contents>
89 </output> 90 </output>
90 <output name="ccode.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/> 91 <output name="ccode.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
91 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/> 92 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
93 <param name="savelog" value="true"/>
92 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
93 </test> 95 </test>
94 <test> <!-- test with default ecoli mask --> 96 <test> <!-- test with default ecoli mask -->
95 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> 97 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
96 <param name="source" value="hist"/> 98 <param name="source" value="hist"/>
102 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/> 104 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
103 </assert_contents> 105 </assert_contents>
104 </output> 106 </output>
105 <output name="ccode.accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/> 107 <output name="ccode.accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
106 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/> 108 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
109 <param name="savelog" value="true"/>
107 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
108 </test> 111 </test>
109 </tests> 112 </tests>
110 <help><![CDATA[ 113 <help><![CDATA[
111 114