Mercurial > repos > bgruening > deeptools

diff bamFingerprint.xml @ 65:9bee2c86eeb1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
author iuc
date Mon, 25 May 2015 05:16:10 -0400
parents f3140d17939e
children 1dbd76a58d8b
line wrap: on
line diff
--- a/bamFingerprint.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamFingerprint.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">bamFingerprint</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         @multiple_input_bams@
@@ -19,8 +18,7 @@
 
             --fragmentLength $fragmentLength
 
-            #set newoutFileName=str($outFileName)+".png"
-            --plotFile $newoutFileName
+            --plotFile $outFileName
 
             #if $output.showOutputSettings == "yes"
                 --plotFileFormat $output.outFileFormat
@@ -46,9 +44,12 @@
                 #if $advancedOpt.minMappingQuality:
                 --minMappingQuality '$advancedOpt.minMappingQuality'
                 #end if
+
+                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                    --plotTitle '$advancedOpt.plotTitle'
+                #end if
+
             #end if
-        ; mv $newoutFileName $outFileName
-        ; rm $temp_dir -rf
 ]]>
     </command>
 
@@ -74,7 +75,7 @@
                 <expand macro="ignoreDuplicates" />
                 <expand macro="minMappingQuality" />
                 <expand macro="skipZeros" />
-
+                <expand macro="plotTitle" />
             </when>
         </conditional>
         <conditional name="output">
@@ -85,7 +86,7 @@
             <when value="no" />
             <when value="yes">
                 <expand macro="input_image_file_format" />
-                <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
+                <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
             </when>
         </conditional>
     </inputs>