Mercurial > repos > bgruening > hicexplorer_hiccorrelate

diff hicCorrelate.xml @ 2:ae2d7e2dfeef draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:12:13 -0400
parents fe0243c46b36
children c153ea23aca8
line wrap: on
line diff
--- a/hicCorrelate.xml	Mon Apr 03 07:08:11 2017 -0400
+++ b/hicCorrelate.xml	Thu Nov 02 11:12:13 2017 -0400
@@ -5,8 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
-<![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
 
         @multiple_input_matrices@
         hicCorrelate
@@ -19,14 +18,14 @@
             #end if
             $log1p
 
-            #if $use_range.select_use_range == "yes_use_range"
+            #if $use_range.select_use_range == "yes_use_range":
                 --range $range_min:$range_max
             #end if
 
             #if $chromosomes:
-                --chromosomes #echo '" "'.join([ '"%s"' % $chrom for $chrom in $chromosomes ])#
+                --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
             #end if
-
+            
             --colorMap $colormap
 
             --outFileNameHeatmap ./heatmap.png
@@ -54,7 +53,9 @@
             </when>
         </conditional>
         <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
-            <param name="chromosome" type="text"/>
+            <param name="chromosome" type="text">
+                <validator type="empty_field" />
+            </param>
         </repeat>
 
         <expand macro="colormap" />
@@ -80,12 +81,28 @@
             <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
             <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
         </test>
+        <test>
+            <repeat name="input_files">
+                <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
+                <param name="mlabel" value="first"/>
+            </repeat>
+            <repeat name="input_files">
+                <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
+                <param name="mlabel" value="second"/>
+            </repeat>
+            
+            <param name="log1p" value="True"/>
+            <param name="colormap" value="jet"/>
+            <param name="method" value="spearman"/>
+            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
+            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 
 **What it does**
 
-Computes pairwise correlations between hic matrices data.
+Computes pairwise correlations between Hi-C matrices data.
 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.