Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 11:f6f0702de3b4

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planemo upload
author jpayne
date Tue, 13 Aug 2019 08:40:57 -0400
parents 00ed20576a29
children 4ac593d4b40f
comparison
equal deleted inserted replaced
10:00ed20576a29 11:f6f0702de3b4
9 <requirement type="package" version="0.7.17">bwa</requirement> 9 <requirement type="package" version="0.7.17">bwa</requirement>
10 <requirement type="package" version="3.12.0">spades</requirement> 10 <requirement type="package" version="3.12.0">spades</requirement>
11 <requirement type="package" version="2.27.1">bedtools</requirement> 11 <requirement type="package" version="2.27.1">bedtools</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 git describe --always ;
15 echo "SeqSero 2 v. 1.0.0" ; 14 echo "SeqSero 2 v. 1.0.0" ;
16 #if $reads.reads_select == 'history' 15 #if $reads.reads_select == 'history'
17 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 16 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
18 #set $forward = $reads.forward 17 #set $forward = $reads.forward
19 #set $reverse = $reads.reverse 18 #set $reverse = $reads.reverse
123 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> 122 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
124 </collection> 123 </collection>
125 </param> 124 </param>
126 <output name="results" file="Seqsero_result_25k_coll.tsv" /> 125 <output name="results" file="Seqsero_result_25k_coll.tsv" />
127 </test> 126 </test>
127 <test>
128 <param name="mode" value="a" />
129 <param name="reads_select" value="history" />
130 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
131 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
132 <output name="results" file="Seqsero_result_25k.tsv" />
133 </test>
128 <!-- <test> 134 <!-- <test>
129 <param name="mode" value="a" /> 135 <param name="mode" value="a" />
130 <param name="reads_select" value="collection" /> 136 <param name="reads_select" value="collection" />
131 <param name="coll"> 137 <param name="coll">
132 <collection type="paired"> 138 <collection type="paired">