diff hicCorrelate.xml @ 7:602a0c6f4bb0 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457

--- a/hicCorrelate.xml	Tue Jan 02 10:16:20 2018 -0500
+++ b/hicCorrelate.xml	Wed Mar 07 03:39:03 2018 -0500
@@ -18,15 +18,15 @@
             #end if
             $log1p
 
-            #if $use_range.select_use_range == "yes_use_range":
-                --range $range_min:$range_max
-            #end if
+            @USE_RANGE@
 
             #if $chromosomes:
                 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
             #end if
-            
-            --colorMap $colormap
+
+            #if $colormap:
+                --colorMap $colormap
+            #end if
 
             --outFileNameHeatmap ./heatmap.png
             --outFileNameScatter ./scatter.png
@@ -41,25 +41,15 @@
         </param>
         <param name="log1p" type="boolean" argument="--log1p"  truevalue="--log1p" falsevalue=""
             label="Use the log1p of the matrix values" help="(--log1p)" />
-        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
-            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
-                <option value="no_use_range">No restriction</option>
-                <option value="yes_use_range">Only consider counts within a range</option>
-            </param>
-            <when value="no_use_range"/>
-            <when value="yes_use_range">
-                <param name="range_min" type="integer" value="" min="0"/>
-                <param name="range_max" type="integer" value="" min="0"/>
-            </when>
-        </conditional>
+
+        <expand macro="use_range" />
+
         <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
             <param name="chromosome" type="text">
                 <validator type="empty_field" />
             </param>
         </repeat>
-
         <expand macro="colormap" />
-
     </inputs>
     <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
         <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
@@ -90,7 +80,7 @@
                 <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"/>
@@ -116,7 +106,7 @@
 - log scale for the values
 - Correlate full matrix or only specific chromosomes
 - Correlate only within a given range.
-- colormap to use:  Colormap_ 
+- colormap to use:  Colormap_
 
 Output
 ------