Mercurial > repos > iuc > mothur_make_fastq

comparison make.fastq.xml @ 5:7c99c22d2334 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 13:39:54 -0400
parents a17148e8865a
children
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4:58a3c5074d9e 5:7c99c22d2334
39 <option value="illumina">Illumina</option> 39 <option value="illumina">Illumina</option>
40 </param> 40 </param>
41 </when> 41 </when>
42 <when value="no"/> 42 <when value="no"/>
43 </conditional> 43 </conditional>
44 <expand macro="param-savelog"/>
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <expand macro="logfile-output"/> 47 <expand macro="logfile-output"/>
47 <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq"> 48 <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq">
48 <change_format><!-- if set, chooseformat.format param should override qfile.ext format --> 49 <change_format><!-- if set, chooseformat.format param should override qfile.ext format -->
63 <assert_contents> 64 <assert_contents>
64 <expand macro="test-fastq-format"/> 65 <expand macro="test-fastq-format"/>
65 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 66 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
66 </assert_contents> 67 </assert_contents>
67 </output> 68 </output>
69 <param name="savelog" value="true"/>
68 <expand macro="logfile-test"/> 70 <expand macro="logfile-test"/>
69 </test> 71 </test>
70 <test><!-- test with quality score format conversion --> 72 <test><!-- test with quality score format conversion -->
71 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 73 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
72 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 74 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
76 <assert_contents> 78 <assert_contents>
77 <expand macro="test-fastq-format"/> 79 <expand macro="test-fastq-format"/>
78 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 80 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
79 </assert_contents> 81 </assert_contents>
80 </output> 82 </output>
83 <param name="savelog" value="true"/>
81 <expand macro="logfile-test"/> 84 <expand macro="logfile-test"/>
82 </test> 85 </test>
83 </tests> 86 </tests>
84 <help><![CDATA[ 87 <help><![CDATA[
85 88