Mercurial > repos > bgruening > deeptools_plot_correlation

changeset 11:cc0acb70ded3 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
author bgruening
date Mon, 25 Jan 2016 14:10:43 -0500
parents 12898c0f81b7
children 82e3789b5e59
files deepTools_macros.xml plotCorrelation.xml static/images/QC_multiBamCoverage_humanSamples.png static/images/QC_multiBamSummary_humanSamples.png test-data/multiBamCoverage_regions.bed test-data/multiBamCoverage_result1.npz test-data/multiBamCoverage_result2.npz test-data/multiBamSummary_regions.bed test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz tool_dependencies.xml
diffstat 11 files changed, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Thu Jan 21 09:58:35 2016 -0500
+++ b/deepTools_macros.xml	Mon Jan 25 14:10:43 2016 -0500
@@ -72,12 +72,12 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.0.0</token>
+    <token name="@WRAPPER_VERSION@">2.0.1.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.0">deepTools</requirement>
+            <requirement type="package" version="2.0.1">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -185,7 +185,7 @@
     <xml name="distanceBetweenBins">
         <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
             label="Distance between bins"
-            help="By default, multiBamCoverage considers consecutive bins of
+            help="By default, multiBamSummary considers consecutive bins of
                 the specified 'Bin size'. However, to reduce the
                 computation time, a larger distance between bins can
                 be given. Larger distances result in fewer bins being
--- a/plotCorrelation.xml	Thu Jan 21 09:58:35 2016 -0500
+++ b/plotCorrelation.xml	Mon Jan 25 14:10:43 2016 -0500
@@ -27,7 +27,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamCoverage tool"/>
+        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary tool"/>
         <expand macro="corMethod" />
 
         <conditional name="plotting_type" >
@@ -71,14 +71,14 @@
     </outputs>
     <tests>
         <test>
-            <param name="corData" value="multiBamCoverage_result1.npz" ftype="deeptools_coverage_matrix" />
+            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
             <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <test>
-            <param name="corData" value="multiBamCoverage_result1.npz" ftype="deeptools_coverage_matrix" />
+            <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="whatToPlot" value="scatterplot" />
             <param name="removeOutliers" value="True" />
@@ -93,10 +93,10 @@
 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions
 and different samples. It can visualize the correlation among samples as scatterplots or as
 a heatmap of correlation coefficients. Further output files are optional.
-The compressed input matrices are easily generated using the "multiBamCoverage" and "multiBigwigSummary" tools.
+The compressed input matrices are easily generated using the "multiBamSummary" and "multiBigwigSummary" tools.
 
 
-.. image:: $PATH_TO_IMAGES/QC_multiBamCoverage_humanSamples.png
+.. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
    :alt: Heatmap of RNA Polymerase II ChIP-seq
 
 
Binary file static/images/QC_multiBamCoverage_humanSamples.png has changed
Binary file static/images/QC_multiBamSummary_humanSamples.png has changed
--- a/test-data/multiBamCoverage_regions.bed	Thu Jan 21 09:58:35 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-chrM	1	10
-chrM	5	15
-chrM	10	20
Binary file test-data/multiBamCoverage_result1.npz has changed
Binary file test-data/multiBamCoverage_result2.npz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBamSummary_regions.bed	Mon Jan 25 14:10:43 2016 -0500
@@ -0,0 +1,3 @@
+chrM	1	10
+chrM	5	15
+chrM	10	20
Binary file test-data/multiBamSummary_result1.npz has changed
Binary file test-data/multiBamSummary_result2.npz has changed
--- a/tool_dependencies.xml	Thu Jan 21 09:58:35 2016 -0500
+++ b/tool_dependencies.xml	Mon Jan 25 14:10:43 2016 -0500
@@ -3,7 +3,7 @@
     <package name="python" version="2.7.10">
         <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="1702876fa731" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="deepTools" version="2.0.1">
+        <repository changeset_revision="cf58f07730a8" name="package_python_2_7_deeptools_2_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>