diff galaxy/riboplot.xml @ 3:8e1efafa6277

Updated version * Bugfix: blue lines in some plots (bar colors were not set correctly) * Cookiecutter template * Additional unit tests * Add plot legend

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy/riboplot.xml	Wed Aug 12 09:27:45 2015 +0100
@@ -0,0 +1,54 @@
+<tool id="riboplot" name="riboplot" version="0.1.0">
+    <description>Plot and output read counts for a single transcript in an alignment (BAM)
+    </description>
+    <requirements>
+        <requirement type="package" version="1.2.1">matplotlib</requirement>
+        <requirement type="package" version="0.8.3">pysam</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">../riboplot/riboplot.py
+    --ribo_file "${ribo_file}"
+    --transcriptome_fasta "${transcriptome_fasta}"
+    --transcript_name "${transcript_name}"
+    #if $rnacov.rnacov_select=="yes"
+        --rna_file "${rna_file}"
+    #end if
+    --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="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
+            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
+            <validator type="empty_field" message="Field requires a value"/>
+            <sanitizer>
+                <valid>
+                    <add value="|"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <conditional name="rnacov">
+            <param name="rnacov_select" type="select" label="Include RNA Coverage">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
+            </when>
+            <when value="no" />
+        </conditional>
+        <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="riboplot (HTML report)"/>
+    </outputs>
+    <help>
+    </help>
+</tool>