Mercurial > repos > youngkim > ezbamqc

changeset 17:161866cee2a2

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
wrapper rename
author youngkim
date Wed, 30 Mar 2016 13:28:47 -0400
parents 736260d32237
children 494b5cd02238
files BAMqc.xml ezBAMQC.xml
diffstat 2 files changed, 108 insertions(+), 109 deletions(-) [+]
line wrap: on
line diff
--- a/BAMqc.xml	Wed Mar 30 13:06:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-<tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >
-
-    <description>
-      perform QC on BAM files of NGS dataset
-    </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 $on_tag_string" /> 
-      <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
-    </outputs>
-
-    <help>
-
-**What it does**
-
-This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample.
-
------
-
-The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
-
-ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
-
-.. _CSHL: `Cold Spring Harbor Laboratory`_
-.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
-.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
-.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
-.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
-
-    </help>
-</tool>
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC.xml	Wed Mar 30 13:28:47 2016 -0400
@@ -0,0 +1,108 @@
+<tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >
+
+    <description>
+      perform QC on BAM files of NGS dataset
+    </description>
+
+    <requirements>
+	<requirement type="package">ezBAMQC</requirement>
+	<requirement type="package">R</requirement>
+    </requirements>
+
+    <command interpreter="sh">
+    
+      ezBAMQC.sh 
+
+      -r '${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 NGS libraries (BAM), and performs rapid quality assessment. 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>
+