# HG changeset patch
# User bgruening
# Date 1491217661 14400
# Node ID f768ce54ee2a98e12c59509f3d0f7b3292b1270e
# Parent  6abd5817e0cd75e0ada65f11ec88884fd293860b
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f

diff -r 6abd5817e0cd -r f768ce54ee2a hicPlotDistVsCounts.xml
--- a/hicPlotDistVsCounts.xml	Thu Mar 30 02:40:49 2017 -0400
+++ b/hicPlotDistVsCounts.xml	Mon Apr 03 07:07:41 2017 -0400
@@ -6,28 +6,44 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="aggressive"><![CDATA[
-        ln -s '$matrix' input_matrix.npz.h5 &&
+        #import re
+        #set matrices_path=[]
+        #set matrices_labels=[]
+        #for $counter, $m, in enumerate($matrices):
+            #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier))
+            ln -f -s '${m}' '${identifier}_${counter}.npz.h5' &&
+            #silent $matrices_path.append("'%s_%s.npz.h5'" % ($identifier, $counter))
+            #silent $matrices_labels.append("'%s'" % ($identifier))
+        #end for
+
         @BINARY@
-            --matrix input_matrix.npz.h5
+            --matrices #echo " ".join($matrices_path)#
+            --labels #echo " ".join($matrices_labels)#
             $skipDiagonal
             --plotFile plot.png
-            #if $plotTitle and $plotTitle is not None:
-                --plotTitle '$plotTitle'
+            #if $plotsize:
+                --plotsize $plotsize
             #end if
-
-            ## special: --chromosomeExclude is optional, but if given needs at least one argument
-            #set chroms = '" "'.join([ str($var.chromosomeExclude) for $var in $chromosomeExclude ])
+            --maxdepth $maxdepth
+            $perchr
+            #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ])
             #if $chromosomeExclude:
                 --chromosomeExclude $chroms
             #end if
 ]]>
     </command>
     <inputs>
-        <param argument="--matrix" type="data" format="h5" label="Hi-C normalized/corrected matrix"/>
+        <param argument="--matrices" type="data" format="h5" multiple="True" label="HiC normalized (corrected) matrices"/>
 
         <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
-        <param argument="--plotTitle" type="text" optional="true" label="Plot title"/>
-        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude">
+        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
+            help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
+        <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
+            help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
+        <param argument="--plotsize" type="text" optional="True" label="Plot size"
+            help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." />
+        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
+            help="This is useful for example to exclude the Y chromosome.">
             <param argument="--chromosomeExclude" type="text" value="" />
         </repeat>
 
@@ -37,25 +53,34 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
+            <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
             <param name="skipDiagonal" value="False"/>
             <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
-            <param name="matrix" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
+            <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
             <param name="skipDiagonal" value="False"/>
-            <param name="plotTitle" value="Excluded chrUextra"/>
+            <param name="perchr" value="True" />
             <repeat name="chromosomeExclude">
                 <param name="chromosomeExclude" value="chrUextra"/>
             </repeat>
-            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
+            <repeat name="chromosomeExclude">
+                <param name="chromosomeExclude" value="chrM"/>
+            </repeat>
+            <repeat name="chromosomeExclude">
+                <param name="chromosomeExclude" value="chr3LHet"/>
+            </repeat>
+            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="15000"/>
         </test>
     </tests>
     <help><![CDATA[
 
 **What it does**
 
-This program makes a distance vs. hi-c counts plot per chromosome.
+This program makes a distance vs. hi-c counts plots. It can use several matrix files to compare
+them. If the `--perchr` option is given, each chromosome is plotted independently. In the case
+of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
+matrices denser matrices are scaled down to match the sum of the smaller matrix.
 
 
 ]]></help>
diff -r 6abd5817e0cd -r f768ce54ee2a involucro
Binary file involucro has changed
diff -r 6abd5817e0cd -r f768ce54ee2a macros.xml
--- a/macros.xml	Thu Mar 30 02:40:49 2017 -0400
+++ b/macros.xml	Mon Apr 03 07:07:41 2017 -0400
@@ -11,7 +11,7 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.7.1</token>
+    <token name="@WRAPPER_VERSION@">1.7.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.13">python</requirement>
diff -r 6abd5817e0cd -r f768ce54ee2a test-data/Li_et_al_2015.h5
Binary file test-data/Li_et_al_2015.h5 has changed
diff -r 6abd5817e0cd -r f768ce54ee2a test-data/hicBuildMatrix_result1.h5
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diff -r 6abd5817e0cd -r f768ce54ee2a test-data/hicCorrectMatrix_result1.npz.h5
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diff -r 6abd5817e0cd -r f768ce54ee2a test-data/hicPlotDistVsCounts_result1.png
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diff -r 6abd5817e0cd -r f768ce54ee2a test-data/hicPlotDistVsCounts_result1_.png
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diff -r 6abd5817e0cd -r f768ce54ee2a test-data/hicPlotDistVsCounts_result2.png
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diff -r 6abd5817e0cd -r f768ce54ee2a test-data/hicSumMatrices_result1.npz.h5
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diff -r 6abd5817e0cd -r f768ce54ee2a test-data/small_test_matrix_50kb_res.h5
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