diff hicCompartmentalization.xml @ 6:ed3dea19c464 draft

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

--- a/hicCompartmentalization.xml	Fri Dec 11 21:40:15 2020 +0000
+++ b/hicCompartmentalization.xml	Tue Mar 16 14:56:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCompartmentalization</token>
@@ -13,9 +13,7 @@
         #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
        
         @BINARY@
-
             --obsexp_matrices $m
-
             --pca '$pca'
             --quantile $quantile
 
@@ -26,21 +24,20 @@
             #end if
             --outliers $outliers
             --outputFileName plot.$image_file_format
-
         && mv plot.$image_file_format plot
 ]]>
     </command>
     <inputs>
         <expand macro="matrix_h5_cooler_multiple_macro" />
-        <param name='pca'  type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with 
-                                no header. In case of several matrices with 
-                                 different conditions, ie. control
-                                treatment, the PCA of control can be 
-                                used. Note that only one PCA can be provided.'/>
-        <param name='quantile'  type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/>
-        <param name='outliers'  type="float"  label="Outliers" help='The number of outliers to be removed.' value="0.0"/>
-        <param name="set_offset_value" type="text" value="" label="Offset values" optional='True'/>
-      
+        <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with no header. In case of several matrices with 
+                    different conditions, ie. control treatment, the PCA of control can be 
+                    used. Note that only one PCA can be provided.' />
+        <param name='quantile' type="integer" value="30" label="Quantile" help='The number of to be used quantiles.' />
+        <param name='outliers' type="float" value="0.0" label="Outliers" help='The number of outliers to be removed.' />
+        <param name="set_offset_value" type="text" optional='True' value="" label="Offset values">
+            <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+        </param>
+
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png" selected="True">png</option>
             <option value="svg">svg</option>
@@ -48,7 +45,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
+        <data name="outFileName" format="png" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
                 <when input="image_file_format" value="pdf" format="pdf" />
@@ -60,21 +57,21 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
-            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
-            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
         </test>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
-            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
-            <param name="quantile" value='30'/>
-            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
+            <param name="quantile" value='30' />
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
         </test>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
-            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
-            <param name="outliers" value='1.0'/>
-            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
+            <param name="outliers" value='1.0' />
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[
@@ -90,6 +87,6 @@
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>