Mercurial > repos > bgruening > deeptools

changeset 34:934b9fccabd4 draft

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Uploaded
author bgruening
date Wed, 29 Jan 2014 19:20:42 -0500 (2014-01-30)
parents fc3830717e24
children 7766dfcd2455
files bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml deepTools_macros.xml heatmapper.xml profiler.xml tool_dependencies.xml
diffstat 12 files changed, 19 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/bamCompare.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/bamCompare.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamCompare</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/bamCorrelate.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/bamCorrelate.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamCorrelate</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/bamCoverage.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/bamCoverage.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamCoverage</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/bamFingerprint.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/bamFingerprint.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamFingerprint</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/bigwigCompare.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/bigwigCompare.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bigwigCompare</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/computeGCBias.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/computeGCBias.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">computeGCBias</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/computeMatrix.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/computeMatrix.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">computeMatrix</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/correctGCBias.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/correctGCBias.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">correctGCBias</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
--- a/deepTools_macros.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/deepTools_macros.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -40,10 +40,11 @@
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
     <xml name="requirements">
         <requirements>
+            <requirement type="binary">@BINARY@</requirement>
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_eabc1c3842f4b6367fb41904061a3b95c9a0ce0c">deepTools</requirement>
+            <requirement type="package" version="1.5.4_570648e1d7a44583a72852f2bd2bf408f76f8f6a">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
@@ -53,6 +54,7 @@
             <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
+        <version_command>@BINARY@ --version</version_command>
     </xml>
     <xml name="stdio">
         <stdio>
--- a/heatmapper.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/heatmapper.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -3,6 +3,7 @@
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">heatmapper</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -177,7 +178,7 @@
                         <option value="yes">Yes, I used multiple regions.</option>
                         <option value="no">No, I used only one region.</option>
                     </param>
-                    <when value="no">
+                    <when value="yes">
                         <conditional name="clustering">
                             <param name="clustering_options" type="select" label="Clustering algorithm">
                                 <option value="none">No clustering</option>
@@ -190,7 +191,7 @@
                             <when value="none" />
                         </conditional>
                     </when>
-                    <when value="yes" />
+                    <when value="no" />
                 </conditional>
             </when>
         </conditional>
--- a/profiler.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/profiler.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -5,6 +5,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">profiler</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -42,11 +43,11 @@
 
             --regionsLabel '$advancedOpt.regionsLabel'
 
-            #if str($advancedOpt.plotTitle.value) != "None":
+            #if str($advancedOpt.plotTitle).strip() != "":
                 --plotTitle '$advancedOpt.plotTitle'
             #end if
 
-            #if str($advancedOpt.colors.value) != "None":
+            #if str($advancedOpt.colors).strip() != "":
                 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
             #end if
 
--- a/tool_dependencies.xml	Tue Jan 28 16:30:41 2014 -0500
+++ b/tool_dependencies.xml	Wed Jan 29 19:20:42 2014 -0500
@@ -57,7 +57,7 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.4_eabc1c3842f4b6367fb41904061a3b95c9a0ce0c">
+    <package name="deepTools" version="1.5.4_570648e1d7a44583a72852f2bd2bf408f76f8f6a">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -79,7 +79,7 @@
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard eabc1c3842f4b6367fb41904061a3b95c9a0ce0c</action>
+                <action type="shell_command">git reset --hard 570648e1d7a44583a72852f2bd2bf408f76f8f6a</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;