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comparison flexbar_dsc.xml @ 29:65103aba4e5f draft

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fix xml
author rnateam
date Thu, 17 Dec 2015 10:58:19 -0500
parents 3d608b751bc4
children 3239487fa9c5
comparison
equal deleted inserted replaced
28:3d608b751bc4 29:65103aba4e5f
11 <requirements> 11 <requirements>
12 <requirement type="package" version="2.5">flexbar</requirement> 12 <requirement type="package" version="2.5">flexbar</requirement>
13 </requirements> 13 </requirements>
14 14
15 <version_command>flexbar --version</version_command> 15 <version_command>flexbar --version</version_command>
16
17 <command><![CDATA[
16 18
17 flexbar 19 flexbar
18 20
19 --threads \${GALAXY_SLOTS:-1} 21 --threads \${GALAXY_SLOTS:-1}
20 22
136 #end if 138 #end if
137 139
138 --target FlexbarOutput && 140 --target FlexbarOutput &&
139 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done && 141 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done &&
140 for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done 142 for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done
141 143 ]]></command>
142
143
144 </command>
145 144
146 145
147 <inputs> 146 <inputs>
148 147
149 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> 148 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
428 identifier in the nested collection and identifier_1 is either 427 identifier in the nested collection and identifier_1 is either
429 forward or reverse (for instance samp1_forward.fq). 428 forward or reverse (for instance samp1_forward.fq).
430 --> 429 -->
431 <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" /> 430 <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" />
432 <!--<data format="txt" name="output" metadata_source="reads"/>--> 431 <!--<data format="txt" name="output" metadata_source="reads"/>-->
432 </collection>
433 </outputs> 433 </outputs>
434 434
435 435
436 <help> 436 <help>
437 437