diff hicAggregateContacts.xml @ 5:ce16a538ab46 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- a/hicAggregateContacts.xml	Mon Dec 16 08:38:26 2019 -0500
+++ b/hicAggregateContacts.xml	Mon Dec 16 15:27:02 2019 -0500
@@ -7,16 +7,17 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-@BINARY@
-    --matrix '$matrix_h5_cooler'
+    ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+    @BINARY@
+    --matrix 'matrix.$matrix_h5_cooler.ext'
     --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
@@ -128,6 +129,8 @@
         <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">
@@ -141,6 +144,8 @@
         <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">
@@ -155,13 +160,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/>
-            <param name="BED" value="test_regions.bed" ftype="bed"/>
+            <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="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" />
+            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/>
         </test>
     </tests>
     <help><![CDATA[