diff ribocount.xml @ 0:ca58e9466cbf

First commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ribocount.xml	Mon Jun 29 16:38:36 2015 +0100
@@ -0,0 +1,31 @@
+<tool id="ribocount" name="ribocount" version="0.1.0">
+    <description>Get read counts for all transcripts in an alignment (BAM)
+    </description>
+    <requirements>
+        <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">./riboplot/ribocount.py
+    --ribo_file "${ribo_file}"
+    --transcriptome_fasta "${transcriptome_fasta}"
+    --read_length "${read_length}"
+    --read_offset "${read_offset}"
+    --html_file "${html_file}"
+    --output_path "${html_file.files_path}"
+    ## --debug
+    </command>
+    <inputs>
+        <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
+        <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
+        <param name="read_length" type="integer" label="Read length to consider" value="28"/>
+        <param name="read_offset" type="integer" label="Offset" value="0"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="html_file" label="ribocount (HTML report)"/>
+    </outputs>
+    <help>
+    </help>
+</tool>