diff chicExportData.xml @ 1:163fd744e235 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788

--- a/chicExportData.xml	Wed Oct 18 17:07:56 2023 +0000
+++ b/chicExportData.xml	Mon Jul 01 20:03:39 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>exports data of hdf to txt based files</description>
     <macros>
         <token name="@BINARY@">chicExportData</token>
@@ -7,7 +7,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         #import re
-        mkdir exportFolder && 
+        mkdir exportFolder &&
         @BINARY@
             --file '$file'
 
@@ -33,13 +33,11 @@
                 --outputModeName $outputMode_conditional.outputModeName
             #end if
             --decimalPlaces $decimalPlaces
-            
             --outFileName exportFolder/export.tar.gz
             --threads @THREADS@
 
-    ]]>    </command>
+    ]]></command>
     <inputs>
-
         <param name="file" type="data" format="h5" label="" />
         <conditional name="fileType_conditional">
        
@@ -59,16 +57,20 @@
                     <when value="txt" >
                     </when>
                     <when value="bigwig" >
-                        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
-                        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
+                        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range"
+                            help="Defines the region upstream of a reference point which should be considered in the analysis." />
+                        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range"
+                            help="Defines the region upstream of a reference point which should be considered in the analysis." />
                         <param name="column_selector" type="select" label="Datatrack output type">
                             <option value="relative-interactions" selected="True">relative interactions</option>
                             <option value="p-value">p-value</option>
                             <option value="x-fold" >x-fold</option>
                             <option value="raw" >raw</option>
                         </param>
-                        <param name="backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
-                        <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size" help="Chromosome size as tabular file. One chromosome per line" />
+                        <param name="backgroundModelFile" type="data" format="tabular" label="Background model"
+                            help="The background file computed by chicViewpointBackgroundModel" />
+                        <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size"
+                            help="Chromosome size as tabular file. One chromosome per line" />
                     </when>
                 </conditional>
             </when>
@@ -136,10 +138,10 @@
                 <param name="outputModeName" value="Eya1" />
             </conditional>
             <output_collection name="oneGeneCollectionBigwig" type="list" count="4">
+                <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
+                <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
                 <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
                 <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
-                <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
-                <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
             </output_collection>
         </test>
         <test expect_num_outputs="2">