Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

diff hicCompareMatrices.xml @ 12:a3d0fb522330 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:23:36 +0000
parents 693fb5e2638e
children
line wrap: on
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--- a/hicCompareMatrices.xml	Tue Jan 10 18:28:37 2023 +0000
+++ b/hicCompareMatrices.xml	Mon Jul 01 19:23:36 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>normalize and compare two Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCompareMatrices</token>
@@ -13,19 +13,21 @@
     --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
     --operation $operation
     --outFileName 'matrix.$matrix1.ext'
-
+    $noNorm
     && mv 'matrix.$matrix1.ext' matrix
 ]]>
     </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>
+        <param name="operation" type="select" label="Operation to be used for the comparison">
+            <option value="diff">diff</option>
             <option value="ratio">ratio</option>
             <option value="log2ratio">log2ratio</option>
         </param>
+        <param name="noNorm" type="boolean" truevalue="--noNorm" falsevalue="" checked="False" label="No normalization" help="Do not apply normalisation before computing the operation" />
+
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
@@ -38,10 +40,10 @@
         <test>
             <param name="matrix1" value="small_test_matrix.h5" />
             <param name="matrix2" value="small_test_matrix.h5" />
-            <param name="operation" value='log2ratio' />
+            <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>