Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

diff hicCompareMatrices.xml @ 11:80abd5e2922a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:11:23 +0000
parents 55b4b8bc250d
children 3ee5332bf57c
line wrap: on
line diff
--- a/hicCompareMatrices.xml	Fri Dec 11 21:35:31 2020 +0000
+++ b/hicCompareMatrices.xml	Tue Mar 16 15:11:23 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>normalize and compare two Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCompareMatrices</token>
@@ -9,7 +9,6 @@
     ln -s '$matrix1' 'matrix1.$matrix1.ext' &&
     ln -s '$matrix2' 'matrix2.$matrix2.ext' &&
 
-
     @BINARY@
     --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
     --operation $operation
@@ -19,10 +18,8 @@
 ]]>
     </command>
     <inputs>
-        <param name='matrix1' type="data" format="h5,cool"
-            label="First matrix"/>
-        <param name='matrix2' type="data" format="h5,cool"
-            label="Second matrix to compare against the first"/>
+        <param name='matrix1' type="data" format="h5,cool" label="First matrix" />
+        <param name='matrix2' type="data" format="h5,cool" label="Second matrix to compare against the first" />
 
         <param name='operation' type='select' label="Operation to be used for the comparison">
             <option value='diff'>diff</option>
@@ -33,24 +30,25 @@
     <outputs>
         <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
             <change_format>
-                <when input_dataset="matrix1" attribute="ext" value="h5" format="h5"/>
+                <when input_dataset="matrix1" attribute="ext" value="h5" format="h5" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="matrix1" value="small_test_matrix.h5"/>
-            <param name="matrix2" value="small_test_matrix.h5"/>
+            <param name="matrix1" value="small_test_matrix.h5" />
+            <param name="matrix2" value="small_test_matrix.h5" />
             <param name="operation" value='log2ratio' />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix'/>
+                    <has_h5_keys keys='intervals,matrix' />
                 </assert_contents>
             </output>
         </test>
 
     </tests>
     <help><![CDATA[
+
 Comparison of Hi-C matrices
 ===========================
 
@@ -92,6 +90,6 @@
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>