diff jamm.xml @ 1:243f75d0ed6e draft default tip

Uploaded. Includes new release 1.0.7 with fixed optional controls.

--- a/jamm.xml	Wed Dec 17 10:40:23 2014 -0500
+++ b/jamm.xml	Thu Feb 19 05:39:45 2015 -0500
@@ -1,20 +1,28 @@
-<tool id="jamm1.0.6rev2" name="JAMM" version="1.0.6.2">
+<tool id="jamm" name="JAMM" version="1.0.7">
 <description>Calls peaks on NGS data</description>
 <requirements>
-<!--
-	<requirement type="package" version="2.5">b2g4pipe</requirement>
--->
+	<requirement>R</requirement>
+	<requirement>perl</requirement>
 </requirements>
 <command interpreter="python">
-jammwrapper.py -i
-	#for $x in $replicate
-	${x.input.file_name}
-	#end for
-	-g ${genomeSizeFile}
-	-z $output
+    <![CDATA[ 
+    jammwrapper.py -i 
+    #for $x in $input
+	${x.replicate.file_name} #end for
+
+    #for $x in $control
+    -c ${x.controlreplicate.file_name} #end for
+    
+    -g ${genomeSizeFile}
+    -o $output
+    -of $outputfiltered
 	-m $mode
 	-r $resolution
-	-p $processes
+    -p $processes
+    -t $type
+    -f $fraglen
+    -b $binsize
+    ]]>
 </command>
 
 <stdio>
@@ -24,12 +32,15 @@
 </stdio>
 
 <inputs>
-	<repeat name="replicate" title="Replicate">
-		<param name="input" type="data" format="bed">
-		</param>
-	</repeat>
-	<param name="genomeSizeFile" type="data" label="File indicating chromosome sizes" description="Chromosome size">
-	</param>
+	<repeat name="input" title="Sample Replicates">
+        <param name="replicate" type="data" format="bed"></param>
+    </repeat>
+
+	<repeat name="control" title="Negative Control Replicates (e.g. input) - optional">
+        <param name="controlreplicate" type="data" format="bed"></param>
+    </repeat>
+
+	<param name="genomeSizeFile" type="data" label="File indicating chromosome sizes" description="Chromosome size"></param>
 	<param name="mode" type="select" label="Mode (normal or narrow)">
      <option value="normal">normal</option>
      <option value="narrow">narrow</option>
@@ -37,19 +48,27 @@
 	<param name="resolution" type="select" label="Resolution (peak or region)">
      <option value="peak">peak</option>
      <option value="region">region</option>
+     <option value="window">window</option>
     </param>
-         
-    <param name="processes"  type="text" value="4" optional="true" help="Number of threads used by R" /> 
+	<param name="type" type="select" label="Type of data (Single or paired. Paired requires BEDPE datasets)">
+     <option value="single" selected="true">single</option>
+     <option value="paired">paired</option>
+    </param>
+    <param name="fraglen"    type="text" value="ns" label="Fragment length. Estimated by default (ns)" /> 
+    <param name="binsize"    type="text" value="ns" label="Bin size. Estimated by default (ns)" />
+    <param name="processes"  type="text" value="4"  label="Number of threads used by R" help="Depending on your Galaxy configuration, 1 should be safe and up to 4 should be fine." /> 
+
 </inputs>
 
 <outputs>
 <data name="output" format="tabular" label="Narrowpeak tabular" />
+<data name="outputfiltered" format="tabular" label="Narrowpeak tabular filtered" />
 </outputs>
 
 <tests>
  <test>
-  <param name="input" value="test1.bed" ftype="bed"/>
-  <param name="input" value="test2.bed" ftype="bed"/>
+  <param name="replicate" value="test1.bed" ftype="bed"/>
+  <param name="replicate" value="test2.bed" ftype="bed"/>
   <param name="genomeSizeFile" value="chrSizes21.csize"/>
   <output name="output" ftype="tabular">
     <assert_contents>
@@ -57,6 +76,18 @@
     </assert_contents>
   </output>
  </test>
+ <test>
+  <param name="replicate" value="test1.bed" ftype="bed"/>
+  <param name="replicate" value="test2.bed" ftype="bed"/>
+  <param name="controlreplicate" value="control.bed" />
+  <param name="genomeSizeFile" value="chrSizes21.csize"/>
+  <param name="resolution"     value="region" />
+  <output name="output" ftype="tabular">
+    <assert_contents>
+      <has_text text="chr21" />
+    </assert_contents>
+  </output>
+ </test>
 </tests>
 
 <citations>
@@ -64,13 +95,23 @@
     <citation type="doi">10.1093/bioinformatics/btu568</citation>
 </citations>    
 <help>
-.. class:: infomark
+**What it does**
+JAMM calls peaks on NGS data, i.e. for finding binding sites.
+
+.. class:: warningmark
 
 This tool requires files in *bed* format.
 
-----
+.. class:: infomark
+
+If you are just starting out, you can find some sensible parameter choices here:
+
+http://code.google.com/p/jamm-peak-finder/wiki/Usage#Examples
 
-**What it does**
-JAMM calls peaks on NGS data, i.e. for finding binding sites.
+* ChIP-Seq TF: everything default
+* ChIP-Seq HM: Binsize=200
+* ChIP-Seq Broad HM: Binsize=200 Resolution=region
+* ChIP-Seq Very Broad HM: Binsize=10000 Resolution=window
+* DNase-seq: Fragment length=1
 </help>
 </tool>