diff chicAggregateStatistic.xml @ 6:b53973719d7b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:19:00 +0000
parents d6f5e51e97ec
children 01c37e54e86e
line wrap: on
line diff
--- a/chicAggregateStatistic.xml	Fri Dec 11 21:29:31 2020 +0000
+++ b/chicAggregateStatistic.xml	Tue Mar 16 15:19:00 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1">
+<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
     <macros>
         <token name="@BINARY@">chicAggregateStatistic</token>
@@ -11,7 +11,6 @@
         mkdir targetFolder &&
         mkdir aggregatedFilesFolder &&
 
-
         #if $tar_input_conditional.tar_input_selector == 'tar_input':
             ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 
             tar -C interactionFiles -xvf viewpoints.tar &&
@@ -30,14 +29,11 @@
                 #set identifier = @ESCAPE_IDENTIFIER_FILE@
                 ln -s '$file' 'targetFolder/$identifier' &&
             #end for
-
         #end if
 
-
         #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
             #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
             #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
-
         #end if
         @BINARY@
             #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
@@ -63,7 +59,7 @@
             && rm -rf aggregatedFilesFolder
         #end if
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
 
         <conditional name="tar_input_conditional">
@@ -72,15 +68,14 @@
                 <option value="interval_input" selected="True">Interval files</option>
             </param>
             <when value="tar_input">
-                <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
-                <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false"/>
+                <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
+                <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false" />
             </when>
             <when value="interval_input">
-                <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
-                <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>
+                <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" />
+                <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true" />
             </when>
         </conditional>
-        
 
         <conditional name="batchmode_conditional">
             <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
@@ -88,20 +83,16 @@
                 <option value="optionSinglemode" selected="True">Single file processing</option>
             </param>
             <when value="optionBatchmode">
-                <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
-                <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order"/>
-
+                <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
+                <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order" />
             </when>
             <when value="optionSinglemode">
             </when>
         </conditional>
-        <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
-                help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
-   
+        <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." />
     </inputs>
     <outputs>
         <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
-        
             <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
         </collection>
         <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
@@ -113,78 +104,73 @@
     </outputs>
     <tests>
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
-            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/>
+            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" />
+            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" />
 
             <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionBatchmode'/>
-                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
-                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
+                <param name="batchmode_selector" value='optionBatchmode' />
+                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
+                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
             </conditional>
 
             <output_collection name="aggregatedFilesCollection" type="list" count="6">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
-
-                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/>
-
-                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" />
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" />
+                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4" />
+                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4" />
+                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4" />
+                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4" />
             </output_collection>
-
-            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
+            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
         </test>
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
-            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt"/>
+            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" />
+            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" />
 
             <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionSinglemode'/>
+                <param name="batchmode_selector" value='optionSinglemode' />
             </conditional>
 
             <output_collection name="aggregatedFilesCollection" type="list" count="2">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" />
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" />
             </output_collection>
         </test>
 
         <test>
             <conditional name="tar_input_conditional">
-                <param name="tar_input_selector" value='interval_input'/>
-                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
-                <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/>
+                <param name="tar_input_selector" value='interval_input' />
+                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" />
+                <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" />
             </conditional>
 
             <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionBatchmode'/>
-                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
-                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
+                <param name="batchmode_selector" value='optionBatchmode' />
+                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
+                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
             </conditional>
-
-            <param name='tar' value='True'/>
-
+            <param name='tar' value='True' />
             <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
-            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
+            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
         </test>
 
-         <test>
+        <test>
             <conditional name="tar_input_conditional">
-                <param name="tar_input_selector" value='tar_input'/>
-                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>
-                <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar"/>
+                <param name="tar_input_selector" value='tar_input' />
+                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" />
+                <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar" />
             </conditional>
 
             <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionBatchmode'/>
-                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
-                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
+                <param name="batchmode_selector" value='optionBatchmode' />
+                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
+                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' />
             </conditional>
 
-            <param name='tar' value='True'/>
+            <param name='tar' value='True' />
 
             <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
-            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
+            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" />
         </test>
     </tests>
     <help><![CDATA[
@@ -199,6 +185,6 @@
 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>