Mercurial > repos > jpetteng > ectyper1_0

comparison ectyper.xml @ 2:338b07ddaa10 draft

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Changed to only use one fastq when paired is selected - otherwise need to make workflow to handle concatenation
author jpetteng
date Wed, 10 Jan 2018 16:12:13 -0500
parents 4724d20b14de
children 4df890ffed44
comparison
equal deleted inserted replaced
1:dbcc6d233eed 2:338b07ddaa10
16 #if $jobtype.select == "asm" 16 #if $jobtype.select == "asm"
17 -i sample.fasta 17 -i sample.fasta
18 #else if $jobtype.select == "se" 18 #else if $jobtype.select == "se"
19 -i sample_1.fastq 19 -i sample_1.fastq
20 #else if $jobtype.select == "pe" 20 #else if $jobtype.select == "pe"
21 -i sample_1.fastq sample_2.fastq 21 -i sample_1.fastq
22 #end if 22 #end if
23 -d $percent_identity 23 -d $percent_identity
24 -l $percent_length 24 -l $percent_length
25 -o "./"; cat ./output/output.csv > results.csv; 25 -o "./"; cat ./output/output.csv > results.csv;
26 26
28 <inputs> 28 <inputs>
29 <conditional name="jobtype"> 29 <conditional name="jobtype">
30 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 30 <param name="select" type="select" label="Assembly or FASTQ Reads?">
31 <option value="asm">Genome Assembly</option> 31 <option value="asm">Genome Assembly</option>
32 <option value="se">Single-End Reads</option> 32 <option value="se">Single-End Reads</option>
33 <option value="pe">Paired-End Reads</option> 33 <option value="pe">Paired-End Reads (only first fastq will be used)</option>
34 </param> 34 </param>
35 <when value="asm"> 35 <when value="asm">
36 <param name="draft" type="data" format="fasta" label="FASTA" /> 36 <param name="draft" type="data" format="fasta" label="FASTA" />
37 </when> 37 </when>
38 <when value="se"> 38 <when value="se">