diff hicMergeDomains.xml @ 2:b376ef118807 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- a/hicMergeDomains.xml	Thu Jan 12 17:55:13 2023 +0000
+++ b/hicMergeDomains.xml	Wed Oct 18 10:49:41 2023 +0000
@@ -42,22 +42,22 @@
 ]]>
     </command>
     <inputs>
-        <param name="domainFiles" type='data' format="bed" multiple="true" label="Domain files from hicFindTADs of different resolutions to include" />
-        <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "In order to be able to better assess the relationship between TADs, the associated protein file (e.g. CTCF for mammals) can be included. The protein file is required in broadpeak forma" />
-        <param argument="--minimumNumberOfPeaks" type="integer" label="Minimum number of peaks" help="Optional parameter to adjust the number of protein peaks when adapting the resolution to the domain files. At least minimumNumberOfPeaks of unique peaks must be in a bin to considered. Otherwise the bin is treated like it has no peaks" value='1' />
-        <param argument="--valueX" type="integer" label="TAD seperation value" help="Determine a value by how much the boundaries of two TADs must at least differ to consider them as two separate TADs" value='5000' />
+        <param name="domainFiles" type="data" format="bed" multiple="true" label="Domain files from hicFindTADs of different resolutions to include" />
+        <param argument="--proteinFile" type="data" format="bed" label="Protein peak file in bed format" help= "In order to be able to better assess the relationship between TADs, the associated protein file (e.g. CTCF for mammals) can be included. The protein file is required in broadpeak forma" />
+        <param argument="--minimumNumberOfPeaks" type="integer" label="Minimum number of peaks" help="Optional parameter to adjust the number of protein peaks when adapting the resolution to the domain files. At least minimumNumberOfPeaks of unique peaks must be in a bin to considered. Otherwise the bin is treated like it has no peaks" value="1" />
+        <param argument="--valueX" type="integer" label="TAD seperation value" help="Determine a value by how much the boundaries of two TADs must at least differ to consider them as two separate TADs" value="5000" />
         <param argument="--percent" type="float" label="Percentage overlap" help="For the relationship determination, a percentage is required from which area coverage the TADs are related to each other. For example, a relationship should be entered from 5 percent area coverage" value="0.5" />
     </inputs>
     <outputs>
-        <data name='outputMergedList' from_work_dir='mergedDomains.bed' format='bed' label='Merged domains' />
-        <data name='outputRelationList' from_work_dir='relationList.txt' format='txt' label='Relationship list' />
+        <data name="outputMergedList" from_work_dir="mergedDomains.bed" format="bed" label="Merged domains" />
+        <data name="outputRelationList" from_work_dir="relationList.txt" format="txt" label="Relationship list" />
         <collection name="plotCollection" type="list" label="Relationship tree plots">
-            <discover_datasets pattern="__name__" format='pdf' directory="relationship_plots" />
+            <discover_datasets pattern="__name__" format="pdf" directory="relationship_plots" />
         </collection>
     </outputs>
     <tests>
         <test>
-            <param name="domainFiles" ftype='bed' value="hicMergeDomains/10kbtad_domains.bed,hicMergeDomains/50kbtad_domains.bed,hicMergeDomains/100kbtad_domains.bed" />
+            <param name="domainFiles" ftype="bed" value="hicMergeDomains/10kbtad_domains.bed,hicMergeDomains/50kbtad_domains.bed,hicMergeDomains/100kbtad_domains.bed" />
 
             <param name="minimumNumberOfPeaks" value="2" />
             <param name="proteinFile" value="hicMergeDomains/ctcf_sorted.bed" />