diff hicAdjustMatrix.xml @ 6:a7fd644deda6 draft

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

--- a/hicAdjustMatrix.xml	Fri Dec 11 21:41:41 2020 +0000
+++ b/hicAdjustMatrix.xml	Tue Mar 16 15:30:48 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>adjust the shape of a Hi-C matrix</description>
     <macros>
         <token name="@BINARY@">hicAdjustMatrix</token>
@@ -22,18 +22,18 @@
         #end if
 
         #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
-                --regions '$chromosomeOrRegionFile_conditional.regions'
+            --regions '$chromosomeOrRegionFile_conditional.regions'
         #end if
 
-        && mv "$matrix_file_out" matrix
+        && mv '$matrix_file_out' matrix
 ]]>
     </command>
     <inputs>
         <expand macro='matrix_h5_cooler_macro' />
-        <param name="action_selector" type="select" label="Apply action" >
-                <option value="keep" selected="True">keep</option>
-                <option value="remove">remove</option>
-                <option value="mask">mask</option>
+        <param name="action_selector" type="select" label="Apply action">
+            <option value="keep" selected="True">keep</option>
+            <option value="remove">remove</option>
+            <option value="mask">mask</option>
         </param>
         <conditional name="chromosomeOrRegionFile_conditional">
             <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions">
@@ -41,58 +41,51 @@
                 <option value="optionRegionFile" selected="True">Region BED file</option>
             </param>
             <when value="optionChromosomes">
-                 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask"
-                    help="The selected option will be applied on the selected chromosomes." >
-                    <param name="chromosome" type="text" >
+                <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" help="The selected option will be applied on the selected chromosomes.">
+                    <param name="chromosome" type="text">
                         <validator type="empty_field" />
                     </param>
                 </repeat>
-
             </when>
             <when value="optionRegionFile">
-                <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered."
-                        help="Should contain the regions which should be kept, removed or masked." />
-
+                <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." />
             </when>
         </conditional>
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="matrix" format="h5">
-             <change_format>
+            <change_format>
                 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
             </change_format>
         </data>
     </outputs>
     <tests>
-        <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+        <test expect_num_outputs="1">
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="action_selector" value="keep" />
             <conditional name="chromosomeOrRegionFile_conditional">
-                <param name="chromosomeOrRegionFile_selector" value='optionChromosomes'/>
+                <param name="chromosomeOrRegionFile_selector" value='optionChromosomes' />
                 <repeat name="chromosomeOrder">
-                    <param name="chromosome" value='chrX'/>
-                    <param name="chromosome" value='chr3R'/>
+                    <param name="chromosome" value='chrX' />
+                    <param name="chromosome" value='chr3R' />
                 </repeat>
             </conditional>
-
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix'/>
+                    <has_h5_keys keys='intervals,matrix' />
                 </assert_contents>
             </output>
         </test>
-
-        <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+        <test expect_num_outputs="1">
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="action_selector" value="mask" />
             <conditional name="chromosomeOrRegionFile_conditional">
-                <param name="chromosomeOrRegionFile_selector" value='optionRegionFile'/>
-                <param name="regions" value='regions.bed'/>
+                <param name="chromosomeOrRegionFile_selector" value='optionRegionFile' />
+                <param name="regions" value='regions.bed' />
             </conditional>
-
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix,nan_bins'/>
+                    <has_h5_keys keys='intervals,matrix,nan_bins' />
                 </assert_contents>
             </output>
         </test>
@@ -109,6 +102,6 @@
 | 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>