diff hicCorrelate.xml @ 21:ec88fad8bc26 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

--- a/hicCorrelate.xml	Fri Dec 11 20:48:28 2020 +0000
+++ b/hicCorrelate.xml	Tue Mar 16 14:02:44 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCorrelate</token>
@@ -35,12 +35,11 @@
     <inputs>
         <expand macro="multiple_input_matrices" />
 
-        <param name="method" type="select" label="Correlation method to use" argument="--method" >
+        <param argument="--method" type="select" label="Correlation method to use">
             <option value="spearman">Spearman</option>
             <option selected="true" value="pearson">Pearson</option>
         </param>
-        <param name="log1p" type="boolean" argument="--log1p"  truevalue="--log1p" falsevalue=""
-            label="Use the log1p of the matrix values" help="If set, then the log1p of the matrix values is used.
+        <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" label="Use the log1p of the matrix values" help="If set, then the log1p of the matrix values is used.
             This parameter has no effect for Spearman correlations
             but changes the output of Pearson correlation and, for
             the scatter plot, if set, the visualization of the
@@ -55,41 +54,41 @@
         </repeat>
         <expand macro="colormap" />
     </inputs>
-    <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
+    <outputs>        <!-- not sure if argument is specifiable for output yet, would be cool if so -->
         <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
         <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
     </outputs>
     <tests>
         <test>
             <repeat name="input_files">
-                <param name="matrix" value="small_test_matrix.h5" ftype="h5"/>
-                <param name="mlabel" value="first"/>
+                <param name="matrix" value="small_test_matrix.h5" ftype="h5" />
+                <param name="mlabel" value="first" />
             </repeat>
             <repeat name="input_files">
                 <param name="matrix" value="small_test_matrix.h5" ftype="h5" />
-                <param name="mlabel" value="second"/>
+                <param name="mlabel" value="second" />
             </repeat>
-            <param name="log1p" value="True"/>
-            <param name="colormap" value="jet"/>
-            <param name="method" value="spearman"/>
-            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
-            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
+            <param name="log1p" value="True" />
+            <param name="colormap" value="jet" />
+            <param name="method" value="spearman" />
+            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size" />
+            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size" />
         </test>
         <test>
             <repeat name="input_files">
-                <param name="matrix" value="small_test_matrix.h5" ftype="h5"/>
-                <param name="mlabel" value="first"/>
+                <param name="matrix" value="small_test_matrix.h5" ftype="h5" />
+                <param name="mlabel" value="first" />
             </repeat>
             <repeat name="input_files">
                 <param name="matrix" value="small_test_matrix.h5" ftype="h5" />
-                <param name="mlabel" value="second"/>
+                <param name="mlabel" value="second" />
             </repeat>
 
-            <param name="log1p" value="True"/>
-            <param name="colormap" value="jet"/>
-            <param name="method" value="spearman"/>
-            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
-            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
+            <param name="log1p" value="True" />
+            <param name="colormap" value="jet" />
+            <param name="method" value="spearman" />
+            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size" />
+            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[
@@ -140,6 +139,6 @@
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html
 
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>