|
1
|
1 <tool id="splice_trap" name="SpliceTrap" version="1.0.0">
|
|
|
2 <description>A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing.
|
|
|
3 </description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="1.2.1.1">bowtie</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command detect_errors="exit_code"><![CDATA[
|
|
|
8 perl $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 "$input1" -2 "$input2" -s "$read_size" "$output1" "$output2"
|
|
|
9 ]]></command>
|
|
|
10 <inputs>
|
|
|
11 <param type="data" name="input1" format="fastq" />
|
|
|
12 <param type="data" name="input2" format="fastq" />
|
|
|
13 <param name='read_size' type='integer' value='50' label="Read size" />
|
|
|
14 </inputs>
|
|
|
15 <outputs>
|
|
|
16 <data name="output1" format="txt" />
|
|
|
17 <data name="output2" format="txt" />
|
|
|
18 </outputs>
|
|
|
19 <tests>
|
|
|
20 <test>
|
|
|
21 <param name="input1" value="input1.fastq"/>
|
|
|
22 <param name="input2" value="input2.fastq"/>
|
|
|
23 <output name="output1" file="output1.txt"/>
|
|
|
24 <output name="output2" file="output2.txt"/>
|
|
|
25 </test>
|
|
|
26 </tests>
|
|
|
27 <help>
|
|
|
28 **SpliceTrap**
|
|
|
29 </help>
|
|
|
30 <citations>
|
|
|
31 <citation type="bibtex">
|
|
|
32 http://rulai.cshl.edu/splicetrap
|
|
|
33 </citation>
|
|
|
34 </citations>
|
|
|
35 </tool>
|
