# HG changeset patch
# User cshl-bsr
# Date 1459354476 14400
# Node ID bee9673b8f46f2376de66e87d3a21ac19e02d8df
# Parent  5bfcc6c131edfbb567b87c39beb6d8a65406f2f6
Uploaded

diff -r 5bfcc6c131ed -r bee9673b8f46 BAMqc.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BAMqc.xml	Wed Mar 30 12:14:36 2016 -0400
@@ -0,0 +1,109 @@
+<tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >
+
+    <description>
+      performs QC on BAM files for gene abundances and sample correlation
+    </description>
+
+    <requirements>
+	<requirement type="package">BAMqc</requirement>
+	<requirement type="package">samtools</requirement>
+	<requirement type="package">R</requirement>
+    </requirements>
+
+    <command interpreter="sh">
+    
+      BAMqc.sh 
+
+      -r '${refdb}'
+
+      -f '${attrID}'
+      
+      -R '${rRNAdb}'
+
+      -s '$stranded'
+
+      -o "$output"
+
+      #set $core = len($files)
+      
+      -p $core
+
+      #if str($cond_adv_options.adv_options) == 'yes':
+        -q '$cond_adv_options.mapq'
+      #end if
+
+      #for $file in $files
+        '$file.input'
+        '$file.input.tag'
+      #end for
+
+    </command>
+
+    <inputs>    
+      <repeat name="files" title="BAM files" min="1">
+        <param format="bam" name="input" type="data" label="Files for QC" />
+      </repeat>
+      
+      <param name="refdb" type="select" label="Reference gene model (GTF)">
+        <options from_data_table="gene_GTF_database" />
+      </param>
+
+      <param name="attrID" type="text" size="50" value="gene_id" label="Feature ID name" help="Summing reads based on gene (gene_id) or transcript (transcript_id.">
+        <sanitizer>
+	  <valid initial="none">
+	    <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." />
+	  </valid>
+	</sanitizer>
+      </param>
+
+      <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)">
+        <options from_data_table="rRNA_BED_database" />
+      </param>
+
+      <param name="stranded" type="select" label="Strandedness">
+        <option value="yes">Yes - Read from stranded library</option>
+        <option value="no">No - Reads from unstranded library</option>
+        <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option>
+     </param>
+            
+       <conditional name="cond_adv_options">
+         <param name="adv_options" type="select" label="Set advanced options">
+	   <option value="no" selected="true">No</option>
+	   <option value="yes">Yes</option>
+	 </param>
+
+	 <when value="yes">
+	   <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" />
+	 </when>
+
+	 <when value="no" />	
+      </conditional>
+
+    </inputs>
+
+    <outputs>
+     <data format="html" name="output" label="BAM QC on $on_tag_string" /> 
+      <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
+    </outputs>
+
+    <help>
+
+**What it does**
+
+This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample.
+
+-----
+
+The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
+
+ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
+
+.. _CSHL: `Cold Spring Harbor Laboratory`_
+.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
+.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
+.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
+.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
+
+    </help>
+</tool>
+