Mercurial > repos > jpayne > snp_pipeline

comparison 1_map_reads.xml @ 43:62531f7399dc

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planemo upload commit 0399c6bd696435a7a99d8d8b4c237e5a78ee5856-dirty
author jpayne
date Wed, 25 Apr 2018 15:54:10 -0400
parents 02733e77f84f
children e7cac7790476
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42:11296a86e01b 43:62531f7399dc
6 <requirement type="package" version="1.5.11">boto3</requirement> 6 <requirement type="package" version="1.5.11">boto3</requirement>
7 <!-- <requirement type="package" version="3.5">python</requirement> --> 7 <!-- <requirement type="package" version="3.5">python</requirement> -->
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
11 env &&
12 #if $reads.reads_select == 'collection' 11 #if $reads.reads_select == 'collection'
13 export files="$reads.coll.forward $reads.coll.reverse" && 12 export files="$reads.coll.forward $reads.coll.reverse" &&
14 export params="-1 $reads.coll.forward -2 $reads.coll.reverse" && 13 export params="-1 $reads.coll.forward -2 $reads.coll.reverse" &&
15 #else 14 #else
16 export files="$forward $reverse" && 15 export files="$forward $reverse" &&
79 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 78 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
80 <option value="collection">Paired collection from your history</option> 79 <option value="collection">Paired collection from your history</option>
81 <option value="history">Two FASTQ datasets from your history</option> 80 <option value="history">Two FASTQ datasets from your history</option>
82 </param> 81 </param>
83 <when value="collection"> 82 <when value="collection">
84 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired" /> 83 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
85 </when> 84 </when>
86 <when value="history"> 85 <when value="history">
87 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger" /> 86 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
88 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger" /> 87 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
89 </when> 88 </when>
90 </conditional> 89 </conditional>
91 </inputs> 90 </inputs>
92 <outputs> 91 <outputs>
93 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam"> 92 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">