Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

diff chicAggregateStatistic.xml @ 2:fb981b15ccef draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 16:58:07 -0400
parents 1baccff6ffb4
children d6f5e51e97ec
line wrap: on
line diff
--- a/chicAggregateStatistic.xml	Wed Feb 05 19:51:27 2020 -0500
+++ b/chicAggregateStatistic.xml	Wed Mar 11 16:58:07 2020 -0400
@@ -11,7 +11,7 @@
         mkdir targetFolder &&
         mkdir aggregatedFilesFolder &&
 
-       
+
         #for $file in $interactionFiles:
             #set identifier = @ESCAPE_IDENTIFIER_FILE@
             ln -s '$file' 'interactionFiles/$identifier' &&
@@ -39,9 +39,9 @@
                 --batchMode
                 --writeFileNamesToFile aggregatedFilesBatch.txt
             #end if
-            
+
             --outputFolder aggregatedFilesFolder
-            -suffix aggregated.bed
+            -suffix aggregated.txt
             --threads @THREADS@
 
     ]]></command>
@@ -55,8 +55,8 @@
                 <option value="optionSinglemode" selected="True">Single file processing</option>
             </param>
             <when value="optionBatchmode">
-                <param name='interactionFilesOrderFile' type="data" format="tabular" label="Interaction file order"/> 
-                <param name='targetFilesOrderFile' type="data" format="tabular" 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">
@@ -73,39 +73,39 @@
     </outputs>
     <tests>
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed"/>
-            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed"/>
-            
+            <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'/>
             </conditional>
-            
+
             <output_collection name="aggregatedFilesCollection" type="list" count="6">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" 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.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" ftype="interval" lines_diff="4"/>
-               
-                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" 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'/>
         </test>
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed"/>
-            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed"/>
-            
+            <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'/>
             </conditional>
-            
+
             <output_collection name="aggregatedFilesCollection" type="list" count="2">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" 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>
     </tests>