diff hicPlotViewpoint.xml @ 13:b637a1e3cb14 draft

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

--- a/hicPlotViewpoint.xml	Fri Dec 11 21:03:00 2020 +0000
+++ b/hicPlotViewpoint.xml	Tue Mar 16 15:02:19 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>plot interactions around a viewpoint</description>
     <macros>
         <token name="@BINARY@">hicPlotViewpoint</token>
@@ -32,53 +32,49 @@
     <inputs>
         <expand macro='matrix_h5_cooler_multiple_macro' />
         <expand macro="region" />
-        <param name="referencePoint" type="text" label="Reference point"
-            help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
-
-        <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
-                            label="Create bedgraph file with interactions" />
+        <param name="referencePoint" type="text" label="Reference point" help="The format is chr:referencePoint or chr:regionStart-regionEnd.">
+            <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
+        </param>
+        <param argument="--interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" label="Create bedgraph file with interactions" />
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png">png</option>
             <option value="svg">svg</option>
         </param>
-
     </inputs>
     <outputs>
-
         <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
             <change_format>
                 <when input="image_file_format" value="png" format="png" />
                 <when input="image_file_format" value="svg" format="svg" />
             </change_format>
         </data>
-
-        <data format="bedgraph" name="interactionFile" >
+        <data format="bedgraph" name="interactionFile">
             <filter>interactionOutFileName</filter>
-            <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true"/>
+            <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true" />
         </data>
-
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000' />
-            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
+            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size" />
         </test>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000-3300000' />
             <param name='interactionOutFileName' value='True' />
-            <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
+            <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size" />
             <output name="interactionFile">
                 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
             </output>
         </test>
     </tests>
     <help><![CDATA[
+
 Plot Viewpoint
 ==============
 
@@ -107,6 +103,6 @@
 | 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>