Mercurial > repos > bgruening > deeptools_bam_correlate

changeset 8:d6ae9280ef21 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41
author bgruening
date Wed, 23 Dec 2015 03:51:51 -0500
parents 49cbd7e6ab07
children b67afe81e29c
files bamCorrelate.xml deepTools_macros.xml static/images/plotCorrelation_galaxy_bw_heatmap_output.png test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/plotPCA_result1.png test-data/profiler_result2.png tool_dependencies.xml
diffstat 9 files changed, 21 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/bamCorrelate.xml	Tue Dec 22 13:39:02 2015 -0500
+++ b/bamCorrelate.xml	Wed Dec 23 03:51:51 2015 -0500
@@ -20,7 +20,7 @@
             --labels '#echo "' '".join($labels)#'
 
             #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts'
+                --outRawCounts '$outFileRawCounts' 
             #end if
 
             #if $mode.modeOpt == "bins":
@@ -45,16 +45,16 @@
 
         <conditional name="mode">
             <param name="modeOpt" type="select" label="Choose computation mode" 
-                    help="In the bins mode, the coverage is computed for equal
+                    help="In the bins mode, the correlation is computed based on equal
                     length bins. In the BED file mode, as list of genomic regions in BED
                     format has to be given. For each region in the BED file the number of
                     overlapping reads is counted in each of the BAM files.
-                    ">
+                    Then the correlation is computed.">
                 <option value="bins" selected="true">Bins</option>
-                <option value="BED-file">Limit calculation to certain regions (BED file)</option>
+                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
             </param>
             <when value="bins">
-                <param name="binSize" type="integer" value="10000" min="1"
+                <param name="binSize" type="integer" value="10000" min="1" 
                     label="Bin size in bp"
                     help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
 
@@ -64,7 +64,7 @@
             <when value="BED-file">
                 <param name="region_file" type="data" format="bed"
                     label="Region file in BED format"
-                    help="Coverage is computed for the number of reads that overlap such regions."/>
+                    help="Correlation is computed for the number of reads that overlap such regions."/>
             </when>
         </conditional>
 
@@ -113,15 +113,7 @@
 **Output files**:
 
 - **score matrix**: a compressed matrix where every row correponds to a genome region (or bin) and each column corresponds to a sample (BAM file)
-- Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)
-
-=======
-
-.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
-   :alt: Heatmap of RNA Polymerase II ChIP-seq
-
-
-You can find more details on the bamCorrelate doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCorrelate.html
+- optional: uncompressed **score matrix** for 
 
 -----
 
--- a/deepTools_macros.xml	Tue Dec 22 13:39:02 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:51:51 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 13:39:02 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:51:51 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 13:39:02 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:51:51 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>