diff hicAggregateContacts.xml @ 3:ece0d567aefc draft

"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"

--- a/hicAggregateContacts.xml	Mon Dec 09 10:33:47 2019 +0000
+++ b/hicAggregateContacts.xml	Mon Dec 16 13:14:03 2019 +0000
@@ -7,17 +7,16 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-    ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
-    @BINARY@
-    --matrix 'matrix.$matrix_h5_cooler.ext'
+@BINARY@
+    --matrix '$matrix_h5_cooler'
     --BED $BED
     #if $BED2:
         --BED2 $BED2
     #end if
 
-    --range '$range_min:$range_max'
+    --range $range_min:$range_max
 
-    --numberOfBins '$numberOfBins'
+    --numberOfBins $numberOfBins
 
     --transform $transform
     --avgType $avgType
@@ -129,8 +128,6 @@
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png" selected="True">png</option>
             <option value="svg">svg</option>
-            <option value="pdf">pdf</option>
-
         </param>
 
         <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
@@ -144,8 +141,6 @@
         <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
-                <when input="image_file_format" value="pdf" format="pdf" />
-
             </change_format>
         </data>
         <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
@@ -160,13 +155,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool"/>
-            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed"/>
+            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/>
+            <param name="BED" value="test_regions.bed" ftype="bed"/>
             <param name="numberOfBins" value="30" />
             <param name="range_max" value="900000" />
             <param name="range_min" value="50000" />
             <param name="image_file_format" value="png" />
-            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/>
+            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[