diff hicAverageRegions.xml @ 6:03d7978293fe draft

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

--- a/hicAverageRegions.xml	Fri Dec 11 20:57:08 2020 +0000
+++ b/hicAverageRegions.xml	Tue Mar 16 14:57:51 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>sums Hi-C contacts around given reference points and computes their average.</description>
     <macros>
         <token name="@BINARY@">hicAverageRegions</token>
@@ -7,7 +7,6 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-
         ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
         @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext'
 
@@ -24,55 +23,51 @@
     </command>
     <inputs>
         <expand macro='matrix_h5_cooler_macro' />
-        <param argument="--regions" type="data" format='bed'
-                        label="Regions to average"
-                        help="BED file which stores a list of regions that are summed and averaged."/>
+        <param argument="--regions" type="data" format='bed' label="Regions to average" help="BED file which stores a list of regions that are summed and averaged." />
 
-         <conditional name="rangeFormat_conditional">
+        <conditional name="rangeFormat_conditional">
             <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
                 <option value="optionGenomicUnits">Range in genomic units</option>
                 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option>
             </param>
             <when value="optionGenomicUnits">
-                 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
-                 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
+                <param name="upstreamRange" type="integer" value="" label="Upstream range" />
+                <param name="downstreamRange" type="integer" value="" label="Downstream range" />
             </when>
             <when value="optionBinUnits">
-                 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
-                 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
+                <param name="upstreamRange" type="integer" value="" label="Upstream range" />
+                <param name="downstreamRange" type="integer" value="" label="Downstream range" />
             </when>
         </conditional>
         <param name="coordinatesToBinMapping_selector" type="select" label="Define start value of range" help="If the region contains start and end coordinates, define if the start, center (start + (end-start) / 2) or end bin should be used as start for range.">
-                <option value="start">Start</option>
-                <option value="center" selected="True">Center</option>
-                <option value="end" selected="True">End</option>
+            <option value="start">Start</option>
+            <option value="center" selected="True">Center</option>
+            <option value="end" selected="True">End</option>
         </param>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/>
+        <data name="outFileName" from_work_dir="output_matrix.npz" format="zip" />
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
             <param name="regions" value="hicAverageRegions/regions.bed" />
             <conditional name="rangeFormat_conditional">
-                <param name="rangeFormat_selector" value='optionGenomicUnits'/>
-                <param name="upstreamRange" value='100000'/>
-                <param name="downstreamRange" value='100000'/>
+                <param name="rangeFormat_selector" value='optionGenomicUnits' />
+                <param name="upstreamRange" value='100000' />
+                <param name="downstreamRange" value='100000' />
             </conditional>
-
-            <output name='outFileName' file='hicAverageRegions/result_range_100000.npz'  ftype="zip" compare="sim_size" delta="20000" />
+            <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" />
         </test>
-       <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
             <param name="regions" value="hicAverageRegions/regions.bed" />
             <conditional name="rangeFormat_conditional">
-                <param name="rangeFormat_selector" value='optionBinUnits'/>
-                <param name="upstreamRange" value='100'/>
-                <param name="downstreamRange" value='100'/>
+                <param name="rangeFormat_selector" value='optionBinUnits' />
+                <param name="upstreamRange" value='100' />
+                <param name="downstreamRange" value='100' />
             </conditional>
-
-            <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz'  ftype="zip" compare="sim_size" delta="20000" />
+            <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" />
         </test>
     </tests>
     <help><![CDATA[
@@ -91,6 +86,6 @@
 | 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>