diff hicMergeDomains.xml @ 0:6b9b4fd51308 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicMergeDomains.xml	Tue Mar 16 19:37:51 2021 +0000
@@ -0,0 +1,87 @@
+<tool id="hicexplorer_hicmergedomains" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Merges TAD domains</description>
+    <macros>
+        <token name="@BINARY@">hicMergeDomains</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        
+            #for $counter, $tadfile in enumerate($domainFiles):
+                ln -s '$tadfile' '${counter}_tad_file.bed' &&
+            #end for
+            #set $m = ' '.join([ '\'%s_tad_file.bed\'' % $counter for $counter, $inputfile in enumerate($domainFiles) ])
+            
+            @BINARY@        
+            
+            --domainFiles $m
+            
+            #if $proteinFile:
+                --proteinFile '$proteinFile'
+            #end if
+
+            #if $minimumNumberOfPeaks:
+                --minimumNumberOfPeaks $minimumNumberOfPeaks
+            #end if
+
+            #if $valueX:
+                --value $valueX
+            #end if
+
+            #if $percent:
+                --percent $percent
+            #end if
+
+            --outputMergedList mergedDomains.bed
+            --outputRelationList relationList.txt
+            --outputTreePlotFormat pdf
+            --outputTreePlotPrefix relationship_tree
+
+            && mkdir relationship_plots
+            && cp relationship_tree_*.pdf relationship_plots
+]]>
+    </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 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' />
+        <collection name="plotCollection" type="list" label="Relationship tree 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="minimumNumberOfPeaks" value="2" />
+            <param name="proteinFile" value="hicMergeDomains/ctcf_sorted.bed" />
+            <param name="valueX" value="5000" />
+            <param name="percent" value="0.7" />
+            <output name="outputMergedList" file="hicMergeDomains/merged_list.bed" ftype="bed" />
+            <output name="outputRelationList" file="hicMergeDomains/relationship.txt" ftype="txt" />
+
+            <output_collection name="plotCollection" type="list" count="1">
+                <element name="relationship_tree_1.pdf" file="hicMergeDomains/ctcf_plot/two_files_plot_1.pdf" ftype="pdf" compare="sim_size" />
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Merge of TAD domains
+====================
+
+Merges and computes the hierachy of TADs from different resolutions.
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_.
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+
+]]>    </help>
+    <expand macro="citations" />
+</tool>