Mercurial > repos > bgruening > deeptools

changeset 35:7766dfcd2455 draft

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Uploaded
author bgruening
date Thu, 30 Jan 2014 19:16:15 -0500
parents 934b9fccabd4
children ea2f64efe70d
files deepTools_macros.xml heatmapper.xml tool_dependencies.xml
diffstat 3 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Wed Jan 29 19:20:42 2014 -0500
+++ b/deepTools_macros.xml	Thu Jan 30 19:16:15 2014 -0500
@@ -44,7 +44,7 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_570648e1d7a44583a72852f2bd2bf408f76f8f6a">deepTools</requirement>
+            <requirement type="package" version="1.5.4_b2b025a382f00f05c46cabc16d2cbe90dbb5d63a">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>
@@ -148,10 +148,10 @@
                 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
                     Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 
                     See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
-                <option value="2150570000">mm9</option>
-                <option value="2451960000">hg19</option>
-                <option value="121400000">dm3</option>
-                <option value="93260000">ce10</option>
+                <option value="2150570000">mm9 (2150570000)</option>
+                <option value="2451960000">hg19 (2451960000)</option>
+                <option value="121400000">dm3 (121400000)</option>
+                <option value="93260000">ce10 (93260000)</option>
                 <option value="specific">user specified</option>
             </param>
             <when value="specific">
--- a/heatmapper.xml	Wed Jan 29 19:20:42 2014 -0500
+++ b/heatmapper.xml	Thu Jan 30 19:16:15 2014 -0500
@@ -81,7 +81,7 @@
 
             $advancedOpt.onePlotPerGroup
 
-            #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'yes':
+            #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
                 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
                     #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
                         --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
@@ -178,7 +178,7 @@
                         <option value="yes">Yes, I used multiple regions.</option>
                         <option value="no">No, I used only one region.</option>
                     </param>
-                    <when value="yes">
+                    <when value="no">
                         <conditional name="clustering">
                             <param name="clustering_options" type="select" label="Clustering algorithm">
                                 <option value="none">No clustering</option>
@@ -191,7 +191,7 @@
                             <when value="none" />
                         </conditional>
                     </when>
-                    <when value="no" />
+                    <when value="yes" />
                 </conditional>
             </when>
         </conditional>
--- a/tool_dependencies.xml	Wed Jan 29 19:20:42 2014 -0500
+++ b/tool_dependencies.xml	Thu Jan 30 19:16:15 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_570648e1d7a44583a72852f2bd2bf408f76f8f6a">
+    <package name="deepTools" version="1.5.4_b2b025a382f00f05c46cabc16d2cbe90dbb5d63a">
         <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 570648e1d7a44583a72852f2bd2bf408f76f8f6a</action>
+                <action type="shell_command">git reset --hard b2b025a382f00f05c46cabc16d2cbe90dbb5d63a</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;