Mercurial > repos > bgruening > deeptools_plot_pca

changeset 11:f173cc2d28f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
author bgruening
date Mon, 25 Jan 2016 14:12:29 -0500
parents 7a9ee42ca6e6
children 9d66351c718e
files deepTools_macros.xml plotPCA.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, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Thu Jan 21 09:59:00 2016 -0500
+++ b/deepTools_macros.xml	Mon Jan 25 14:12:29 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/plotPCA.xml	Thu Jan 21 09:59:00 2016 -0500
+++ b/plotPCA.xml	Mon Jan 25 14:12:29 2016 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0">
-    <description>generate a principal component analysis (PCA) plot from multiBamCoverage or multiBigwigSummary output</description>
+    <description>generate a principal component analysis (PCA) plot from multiBamSummary or multiBigwigSummary output</description>
     <macros>
         <token name="@BINARY@">plotPCA</token>
         <import>deepTools_macros.xml</import>
@@ -15,7 +15,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamCoverage or multiBigwigSummary tools"/>
+        <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
         <expand macro="input_image_file_format" />
         <expand macro="plotTitle" />
     </inputs>
@@ -24,7 +24,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="corData" value="multiBamCoverage_result2.npz" ftype="deeptools_coverage_matrix" />
+            <param name="corData" value="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <output name="outFileName" file="plotPCA_result1.png" ftpye="png" compare="sim_size" delta="100" />
@@ -36,7 +36,7 @@
 **What it does**
 
 Tool for generating a principal component analysis (PCA)
-plot from multiBamCoverage or multiBigwigSummary output.
+plot from multiBamSummary or multiBigwigSummary output.
 
 -----
 
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 09:59:00 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 14:12:29 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 09:59:00 2016 -0500
+++ b/tool_dependencies.xml	Mon Jan 25 14:12:29 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>