diff splice_trap.xml @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splice_trap.xml	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,35 @@
+<tool id="splice_trap" name="SpliceTrap" version="1.0.0">
+    <description>A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing.
+    </description>
+    <requirements>
+        <requirement type="package" version="1.2.1.1">bowtie</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        perl $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 "$input1" -2 "$input2" -s "$read_size" "$output1" "$output2"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fastq" />
+        <param type="data" name="input2" format="fastq" />
+        <param name='read_size' type='integer' value='50' label="Read size"  />
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" />
+        <data name="output2" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input1.fastq"/>
+            <param name="input2" value="input2.fastq"/>
+            <output name="output1" file="output1.txt"/>
+            <output name="output2" file="output2.txt"/>
+        </test>
+    </tests>
+    <help> 
+        **SpliceTrap**
+    </help>
+    <citations>
+        <citation type="bibtex">
+            http://rulai.cshl.edu/splicetrap
+        </citation>
+    </citations>
+</tool>