changeset 6:81f8efdc1f7b draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

--- a/correctGCBias.xml	Tue Dec 22 13:45:40 2015 -0500
+++ b/correctGCBias.xml	Wed Dec 23 03:58:23 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
-    <description>uses the output from computeGCBias to generate GC-corrected BAM files</description>
+    <description>uses the output from computeGCBias to generate corrected BAM files</description>
     <macros>
         <token name="@BINARY@">correctGCBias</token>
         <import>deepTools_macros.xml</import>
@@ -59,7 +59,7 @@
 Benjamini and Speed (2012) Nucleic Acids Res.
 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
 
-You can find more details on the correctGCBias doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/correctGCBias.html
+You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
 
 
 **Output files**:

--- a/deepTools_macros.xml	Tue Dec 22 13:45:40 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:58:23 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,11 +107,7 @@
                     </param>
                     <when value="kmeans">
                         <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
-                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm.
-                            Only works for data that is not grouped, otherwise only the first group will be clustered.
-                            If more specific clustering methods are required it is advisable to save the underlying matrix and
-                            run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault)
-                            if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/>
+                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -412,6 +408,7 @@
             <when value="no" />
             <when value="yes">
                 <yield />
+                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
             </when>
         </conditional>
@@ -459,6 +456,14 @@
     </xml>
 
     <xml name="output_graphic_outputs">
+        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveData'] is True
+            ))
+            </filter>
+        </data>
         <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
             <filter>
             ((

Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed

Binary file test-data/bamCoverage_result1.bw has changed

Binary file test-data/bamCoverage_result2.bw has changed

--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:45:40 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:58:23 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	16569	623538.2
+chrM	250	260	623538.19

Binary file test-data/plotPCA_result1.png has changed

Binary file test-data/profiler_result2.png has changed

--- a/tool_dependencies.xml	Tue Dec 22 13:45:40 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:58:23 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.0">
-        <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>