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Use GALAXY_SLOTS for multithreading in Bowtie. Create symlinks instead of copying files. Specify in help that Bowtie is used to align the reads to the contigs. Add readme.rst .
author crs4
date Mon, 03 Mar 2014 11:28:41 -0500
parents 988d5a82291a
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1:d180348fe9db 2:87ffe493b6c1
1 <tool id="sopra_wpc" name="SOPRA with prebuilt contigs" version="0.1"> 1 <tool id="sopra_wpc" name="SOPRA with prebuilt contigs" version="0.1">
2 <description>for Illumina workflow</description> 2 <description>for Illumina libraries</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.6">sopra</requirement> 4 <requirement type="package" version="1.4.6">sopra</requirement>
5 <requirement type="package" version="1.0.0">bowtie</requirement> 5 <requirement type="package" version="1.0.0">bowtie</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <command interpreter="python">
8 sopra_wpc.py 8 sopra_wpc.py -p \${GALAXY_SLOTS:-1}
9 #for $cr in $contigs_repeat 9 #for $cr in $contigs_repeat
10 --contigs ${cr.contigs_file} 10 --contigs ${cr.contigs_file}
11 #end for 11 #end for
12 #for $mr in $mate_repeat 12 #for $mr in $mate_repeat
13 --mate ${mr.mate_file} 13 --mate ${mr.mate_file}
34 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/> 34 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
35 </outputs> 35 </outputs>
36 <help> 36 <help>
37 **What it does** 37 **What it does**
38 38
39 SOPRA is an assembly tool for mate pair/paired-end data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms. 39 SOPRA is a scaffold assembly tool for paired-end/mate pair data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms. This wrapper currently supports only Illumina paired-end data.
40
41 Bowtie is used to align the reads to the contigs.
40 42
41 The input paired-end FASTA file can be obtained with: 43 The input paired-end FASTA file can be obtained with:
42 FR reads -> *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter 44 FR reads -> *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter
43 RF reads -> *Reverse-Complement*, *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter 45 RF reads -> *Reverse-Complement*, *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter
44 46