Mercurial > repos > iuc > hicexplorer_hicmergedomains

comparison hicMergeDomains.xml @ 0:c6b1d11c7363 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:36:39 +0000
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-1:000000000000 0:c6b1d11c7363
1 <tool id="hicexplorer_hicmergedomains" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Merges TAD domains</description>
3 <macros>
4 <token name="@BINARY@">hicMergeDomains</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 #for $counter, $tadfile in enumerate($domainFiles):
11 ln -s '$tadfile' '${counter}_tad_file.bed' &&
12 #end for
13 #set $m = ' '.join([ '\'%s_tad_file.bed\'' % $counter for $counter, $inputfile in enumerate($domainFiles) ])
14
15 @BINARY@
16
17 --domainFiles $m
18
19 #if $proteinFile:
20 --proteinFile '$proteinFile'
21 #end if
22
23 #if $minimumNumberOfPeaks:
24 --minimumNumberOfPeaks $minimumNumberOfPeaks
25 #end if
26
27 #if $valueX:
28 --value $valueX
29 #end if
30
31 #if $percent:
32 --percent $percent
33 #end if
34
35 --outputMergedList mergedDomains.bed
36 --outputRelationList relationList.txt
37 --outputTreePlotFormat pdf
38 --outputTreePlotPrefix relationship_tree
39
40 && mkdir relationship_plots
41 && cp relationship_tree_*.pdf relationship_plots
42 ]]>
43 </command>
44 <inputs>
45 <param name="domainFiles" type='data' format="bed" multiple="true" label="Domain files from hicFindTADs of different resolutions to include" />
46 <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" />
47 <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' />
48 <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' />
49 <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" />
50 </inputs>
51 <outputs>
52 <data name='outputMergedList' from_work_dir='mergedDomains.bed' format='bed' label='Merged domains' />
53 <data name='outputRelationList' from_work_dir='relationList.txt' format='txt' label='Relationship list' />
54 <collection name="plotCollection" type="list" label="Relationship tree plots">
55 <discover_datasets pattern="__name__" format='pdf' directory="relationship_plots" />
56 </collection>
57 </outputs>
58 <tests>
59 <test>
60 <param name="domainFiles" ftype='bed' value="hicMergeDomains/10kbtad_domains.bed,hicMergeDomains/50kbtad_domains.bed,hicMergeDomains/100kbtad_domains.bed" />
61
62 <param name="minimumNumberOfPeaks" value="2" />
63 <param name="proteinFile" value="hicMergeDomains/ctcf_sorted.bed" />
64 <param name="valueX" value="5000" />
65 <param name="percent" value="0.7" />
66 <output name="outputMergedList" file="hicMergeDomains/merged_list.bed" ftype="bed" />
67 <output name="outputRelationList" file="hicMergeDomains/relationship.txt" ftype="txt" />
68
69 <output_collection name="plotCollection" type="list" count="1">
70 <element name="relationship_tree_1.pdf" file="hicMergeDomains/ctcf_plot/two_files_plot_1.pdf" ftype="pdf" compare="sim_size" />
71 </output_collection>
72 </test>
73 </tests>
74 <help><![CDATA[
75
76 Merge of TAD domains
77 ====================
78
79 Merges and computes the hierachy of TADs from different resolutions.
80
81 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
82
83 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
84
85 ]]> </help>
86 <expand macro="citations" />
87 </tool>