diff hicTransform.xml @ 2:3106dcd651f5 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

--- a/hicTransform.xml	Tue Jan 02 10:17:50 2018 -0500
+++ b/hicTransform.xml	Wed Jan 03 13:31:00 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description>
     <macros>
         <token name="@BINARY@">hicTransform</token>
@@ -10,13 +10,10 @@
 
         hicTransform --matrix '$matrix_h5_cooler'
         --method all
-
-        #if $outputFormat == 'h5'
-            --outFileName matrix.h5
-        #elif $outputFormat == 'cool'
-            --outFileName matrix.cool
-        #end if
-
+        --outFileName matrix.$outputFormat
+        && mv obs_exp_matrix.$outputFormat obs_exp_matrix
+        && mv pearson_matrix.$outputFormat pearson_matrix
+        && mv covariance_matrix.$outputFormat covariance_matrix
 ]]>
     </command>
     <inputs>
@@ -28,23 +25,20 @@
 
     </inputs>
     <outputs>
-        <data name="obs_exp_h5" from_work_dir="obs_exp_matrix.h5" format="h5">
-            <filter>outputFormat == 'h5'</filter>
-        </data>
-        <data name="pearson_h5" from_work_dir="pearson_matrix.h5" format="h5">
-            <filter>outputFormat == 'h5'</filter>
-        </data>
-        <data name="covariance_h5" from_work_dir="covariance_matrix.h5" format="h5">
-            <filter>outputFormat == 'h5'</filter>
+        <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5">
+            <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
         </data>
-        <data name="obs_exp_cool" from_work_dir="obs_exp_matrix.cool" format="cool">
-            <filter>outputFormat == 'cool'</filter>
+        <data name="pearson" from_work_dir="pearson_matrix" format="h5">
+            <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
         </data>
-        <data name="pearson_cool" from_work_dir="pearson_matrix.cool" format="cool">
-            <filter>outputFormat == 'cool'</filter>
-        </data>
-        <data name="covariance_cool" from_work_dir="covariance_matrix.cool" format="cool">
-            <filter>outputFormat == 'cool'</filter>
+        <data name="covariance" from_work_dir="covariance_matrix" format="h5">
+            <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
         </data>
 
     </outputs>
@@ -52,16 +46,16 @@
         <test>
             <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
             <param name="outputFormat" value="h5" />
-            <output name="obs_exp_h5" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
-            <output name="pearson_h5" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
-            <output name="covariance_h5" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="obs_exp" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="pearson" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="covariance" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
         </test>
         <test>
             <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
             <param name="outputFormat" value="cool" />
-            <output name="obs_exp_cool" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
-            <output name="pearson_cool" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/>
-            <output name="covariance_cool" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="obs_exp" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="pearson" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="covariance" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[