diff hicPlotDistVsCounts.xml @ 18:e2971589184b draft

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

--- a/hicPlotDistVsCounts.xml	Fri Dec 11 21:14:45 2020 +0000
+++ b/hicPlotDistVsCounts.xml	Tue Mar 16 14:49:02 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>compute distance vs Hi-C counts plot per chromosome</description>
     <macros>
         <token name="@BINARY@">hicPlotDistVsCounts</token>
@@ -37,61 +37,58 @@
 ]]>
     </command>
     <inputs>
-        <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices"/>
+        <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices" />
 
-        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts"
-            help="If set, diagonal counts are not included"/>
-        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
-            help="If more than one Hi-C matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
-        <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
-            help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
-        <param argument="--plotsize" type="text" optional="True" label="Plot size"
-            help="Width and height of the plot (in inches). Default is 6 * number of cols, 4 * number of rows. The maximum number of rows is 4. Example: 6 5." />
-        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
-            help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
-            <param argument="--chromosomeExclude" type="text" value="" >
+        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" help="If set, diagonal counts are not included" />
+        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" help="If more than one Hi-C matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
+        <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
+        <param argument="--plotsize" type="text" optional="True" label="Plot size" help="Width and height of the plot (in inches). Default is 6 * number of cols, 4 * number of rows. The maximum number of rows is 4. Example: 6 5.">
+            <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+        </param>
+        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
+            <param argument="--chromosomeExclude" type="text" value="">
                 <validator type="empty_field" />
             </param>
         </repeat>
-        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData'  falsevalue="" checked="false" label="Save data underlying the plots as BAM"
-            help="A bam file containing all data underlying the plots is saved on this file."/>
+        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." />
     </inputs>
     <outputs>
-        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
+        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot" />
         <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
             <filter>outFileData_Boolean</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="matrices" ftype="h5" value="small_test_matrix.h5"/>
-            <param name="skipDiagonal" value="False"/>
-            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
+            <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
+            <param name="skipDiagonal" value="False" />
+            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
         </test>
         <test>
-            <param name="matrices" ftype="h5" value="small_test_matrix.h5"/>
-            <param name="skipDiagonal" value="False"/>
-            <param name='outFileData_Boolean' value='True'/>
-            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
-            <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/>
+            <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
+            <param name="skipDiagonal" value="False" />
+            <param name='outFileData_Boolean' value='True' />
+            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
+            <output name="outFileData" file="distVsCounts.txt" ftype="txt" />
         </test>
         <test>
-            <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5"/>
-            <param name="skipDiagonal" value="False"/>
+            <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5" />
+            <param name="skipDiagonal" value="False" />
             <param name="perchr" value="True" />
             <repeat name="chromosomeExclude">
-                <param name="chromosomeExclude" value="chrUextra"/>
+                <param name="chromosomeExclude" value="chrUextra" />
             </repeat>
             <repeat name="chromosomeExclude">
-                <param name="chromosomeExclude" value="chrM"/>
+                <param name="chromosomeExclude" value="chrM" />
             </repeat>
             <repeat name="chromosomeExclude">
-                <param name="chromosomeExclude" value="chr3LHet"/>
+                <param name="chromosomeExclude" value="chr3LHet" />
             </repeat>
-            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
+            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[
+
 Relation of genomic distance and number of contacts
 ===================================================
 
@@ -133,6 +130,6 @@
 | 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>