Mercurial > repos > bgruening > deeptools_bam_compare

changeset 11:8f2a1286b61c draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
author bgruening
date Tue, 24 Jan 2017 04:59:05 -0500
parents 9cc3a577f80d
children bda8b9986fae
files bamCompare.xml deepTools_macros.xml repository_dependencies.xml tool_dependencies.xml
diffstat 4 files changed, 13 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/bamCompare.xml	Mon Dec 05 08:12:20 2016 -0500
+++ b/bamCompare.xml	Tue Jan 24 04:59:05 2017 -0500
@@ -114,6 +114,7 @@
                 <option value="ratio">Compute the ratio of the number of reads</option>
                 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
                 <option value="add">Compute the sum of number of reads</option>
+                <option value="mean">Compute the mean of the number of reads between the two files</option>
                 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
                 <option value="first">Returns the scaled value of the first BAM file</option>
                 <option value="second">Returns the scaled value of the second BAM file</option>
@@ -125,6 +126,7 @@
                 <expand macro="pseudocount" />
             </when>
             <when value="add" />
+            <when value="mean" />
             <when value="first" />
             <when value="second" />
             <when value="reciprocal_ratio">
--- a/deepTools_macros.xml	Mon Dec 05 08:12:20 2016 -0500
+++ b/deepTools_macros.xml	Tue Jan 24 04:59:05 2017 -0500
@@ -98,11 +98,11 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.4.1</token>
+    <token name="@WRAPPER_VERSION@">2.4.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="package" version="2.4.1">deeptools</requirement>
+            <requirement type="package" version="2.4.2">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -299,7 +299,7 @@
         <param argument="--sortRegions" type="select" label="Sort regions"
             help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
             <option value="no">no ordering</option>
-            <option value="descend">descending order</option>
+            <option value="descend" selected="true">descending order</option>
             <option value="ascend">ascending order</option>
         </param>
     </xml>
@@ -450,10 +450,10 @@
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
-                ln -s "${f.bamfile}" "./${counter}.bam" &&
-                ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+                ln -s "${f.bamfiles}" "./${counter}.bam" &&
+                ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($f.bamfile.display_name))
+                #silent $labels.append("'%s'" % ($f.bamfiles.display_name))
             #end for
         #end if
 ]]>
@@ -471,9 +471,9 @@
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
-                ln -s "${f.bigwig}" "${counter}.bw" &&
+                ln -s "${f.bigwigfiles}" "${counter}.bw" &&
                 #silent $files.append('%s.bw' % $counter)
-                #silent $labels.append("'%s'" % ($f.bigwig.display_name))
+                #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
             #end for
         #end if
 ]]>
--- a/repository_dependencies.xml	Mon Dec 05 08:12:20 2016 -0500
+++ b/repository_dependencies.xml	Tue Jan 24 04:59:05 2017 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="74b09c8e5f6e" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="df883cc67fbd" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
--- a/tool_dependencies.xml	Mon Dec 05 08:12:20 2016 -0500
+++ b/tool_dependencies.xml	Tue Jan 24 04:59:05 2017 -0500
@@ -3,7 +3,7 @@
     <package name="python" version="2.7.10">
         <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deeptools" version="2.4.1">
-        <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="deeptools" version="2.4.2">
+        <repository changeset_revision="efc55c226f11" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>