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comparison shigatyper.xml @ 6:005fdb74636e tip

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author jpayne
date Fri, 12 Jun 2020 15:07:35 -0400
parents b4e604288530
children
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5:b4e604288530 6:005fdb74636e
7 #if $reads.reads_select == 'collection' 7 #if $reads.reads_select == 'collection'
8 #set forward=$reads.coll.forward 8 #set forward=$reads.coll.forward
9 #set reverse=$reads.coll.reverse 9 #set reverse=$reads.coll.reverse
10 #set name=$reads.coll.name 10 #set name=$reads.coll.name
11 #else 11 #else
12 #set name=$reads.coll.forward.name.split('_')[0] 12 #set name=$forward.name.split('_')[0]
13 #end if 13 #end if
14 14
15 shigatyper -n "$name" "$forward" "$reverse" -vv > 15 shigatyper -n "$name" "$forward" "$reverse" -vv >
16 16
17 #if $reads.reads_select == 'collection' 17 #if $reads.reads_select == 'collection'
51 <output name="serotype_from_history" file="output.tabular"/> 51 <output name="serotype_from_history" file="output.tabular"/>
52 </test> 52 </test>
53 <test> 53 <test>
54 <param name="reads_select" value="collection" /> 54 <param name="reads_select" value="collection" />
55 <param name="coll"> 55 <param name="coll">
56 <collection type="paired"> 56 <collection type="paired" name="CFSAN029786">
57 <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" /> 57 <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" />
58 <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" /> 58 <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" />
59 </collection> 59 </collection>
60 </param> 60 </param>
61 <output name="serotype_from_collection" value="output.tabular" /> 61 <output name="serotype_from_collection" value="output.tabular" />