Mercurial > repos > cstrittmatter > skesa

comparison skesa.xml @ 21:8bafd3d18864 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author cstrittmatter
date Mon, 17 Sep 2018 06:49:22 -0400
parents a368d48a4562
children 9448df7c25a0
comparison
equal deleted inserted replaced
20:a368d48a4562 21:8bafd3d18864
1 <tool id="skesa" name="skesa" version="0.1"> 1 <tool id="skesa" name="skesa" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="2.2">skesa</requirement> 3 <requirement type="package" version="2.2">skesa</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 #if $jobtype.select != "cl" 6
7 skesa 7 skesa
8 #if $jobtype.select == "asm" 8 #if $jobtype.select == "asm"
9 --fasta $draft 9 --fasta $draft
10 #else if $jobtype.select == "se" 10 #else if $jobtype.select == "se"
11 --fastq $fastq1 11 --fastq $fastq
12 #else if $jobtype.select == "cl"
13 #set forward=$jobtype.coll.forward
14 #set reverse=$jobtype.coll.reverse
15 --fastq $forward,$reverse --use_paired_ends
12 #else if $jobtype.select == "pe" 16 #else if $jobtype.select == "pe"
13 --fastq $fastq1,$fastq2 --use_paired_ends 17 --fastq $forward,$reverse --use_paired_ends
18
14 #end if 19 #end if
15 #if $cores != 0 20 #if $cores != 0
16 --cores $cores 21 --cores $cores
17 #end if 22 #end if
18 --memory $memory > results.skesa.fasta 23 --memory $memory > results.skesa.fasta
19 #end if 24
20 25
21 ]]></command> 26 ]]></command>
22 <inputs> 27 <inputs>
23 <conditional name="jobtype"> 28 <conditional name="jobtype">
24 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 29 <param name="select" type="select" label="Assembly or FASTQ Reads?">
25 <option value="asm">Genome Assembly</option> 30 <option value="asm">Genome Assembly</option>
26 <option value="se">Single-End Reads</option> 31 <option value="se">Single-End Reads</option>
27 <option value="pe">Paired-End Reads (Separate Files)</option> 32 <option value="pe">Paired-End Reads (Separate Files)</option>
33 <option value="cl">Paired collection from your history</option>
28 </param> 34 </param>
29 <when value="asm"> 35 <when value="asm">
30 <param name="draft" type="data" format="fasta" label="FASTA" /> 36 <param name="draft" type="data" format="fasta" label="FASTA" />
31 </when> 37 </when>
32 <when value="se"> 38 <when value="se">
33 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 39 <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
40 </when>
41 <when value="cl">
42 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
34 </when> 43 </when>
35 <when value="pe"> 44 <when value="pe">
36 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 45 <param name="forward" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
37 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> 46 <param name="reverse" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
38 </when> 47 </when>
39 </conditional> 48 </conditional>
40 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> 49 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
41 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" /> 50 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
42 51