Mercurial > repos > yufei-luo > s_mart

comparison SMART/DiffExpAnal/gsnap.xml @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 <tool id="gsnap" name="gsnap">
2
3 <description>GSNAP version 2012-12-20.
4 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
5 GSNAP: Genomic Short-read Nucleotide Alignment Program
6 </description>
7
8 <command interpreter="python"> wrappGSNAP.py
9 -d $genomeName -i $inputFasta -k $kmer -q $inputFastq -A $outputFormat -o $outputSam
10
11 #if $optionPairedEnd.paire == 'Yes':
12 -p $optionPairedEnd.pairedEndFile
13 #end if
14
15 </command>
16
17 <inputs>
18 <param name="inputFasta" type="data" format="fasta" label="Reference genome file, fasta format."/>
19 <param name="genomeName" type="text" value="Arabidopsis_Thaliana" label="Please give the reference genome a name! (Ex. Arabidopsis_Thaliana)"/>
20 <param name="kmer" type="integer" value="12" label="Choose kmer value (superior or egal at 16), a big kmer value can take more RAM(4Go)." />
21 <param name="inputFastq" type="data" format="fastq" label="Input fastq file."/>
22 <param name="outputFormat" type="text" format="sam" label="Choose an output format [sam, goby (need to re-compile with appropriate options)]."/>
23
24 <conditional name="optionPairedEnd">
25 <param name="paire" type="select" label="pairedEnd fastq file">
26 <option value="Yes">Yes</option>
27 <option value="No" selected="true">No</option>
28 </param>
29 <when value="Yes">
30 <param name="pairedEndFile" type="data" format="fastq"/>
31 </when>
32 <when value="No">
33 </when>
34 </conditional>
35
36 </inputs>
37
38 <outputs>
39 <data format="sam" name="outputSam" label="gsnap Output"/>
40 </outputs>
41
42 </tool>