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comparison hicBuildMatrix.xml @ 0:9767c021cd58 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:30:47 -0400
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children eb0d14cdf8b8
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-1:000000000000 0:9767c021cd58
1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>creates a matrix of interactions</description>
3 <macros>
4 <token name="@BINARY@">hicBuildMatrix</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" >
8 <requirement type="package" version="1.3.1">samtools</requirement>
9 </expand>
10 <command>
11 <![CDATA[
12
13 mkdir ./QCfolder &&
14 mkdir $qc.files_path
15 &&
16
17 hicBuildMatrix
18
19 --samFiles
20 #for $repeat in $samFiles:
21 '${repeat.samFile}'
22 #end for
23
24 #if $binSize:
25 --binSize $binSize
26 #end if
27
28 #if $restrictionCutFile:
29 --restrictionCutFile '$restrictionCutFile'
30 #end if
31
32 #if $minDistance:
33 --minDistance $minDistance
34 #end if
35
36 #if $maxDistance:
37 --maxDistance $maxDistance
38 #end if
39
40 #if $restrictionSequence:
41 --restrictionSequence '$restrictionSequence'
42 #end if
43
44 #if $region:
45 --region '$region'
46 #end if
47
48 --outFileName ./matrix.h5
49 --outBam ./unsorted.bam
50
51 #if $restrictionCutFile:
52 --restrictionCutFile '$restrictionCutFile'
53 #end if
54
55 $removeSelfCircles
56
57 #if $minMappingQuality and $minMappingQuality is not None:
58 --minMappingQuality $minMappingQuality
59 #end if
60
61 --QCfolder ./QCfolder
62 &&
63 mv ./QCfolder/* $qc.files_path/
64 &&
65 mv $qc.files_path/hicQC.html $qc
66 &&
67 samtools sort ./unsorted.bam -o sorted.bam
68
69 ]]>
70 </command>
71 <inputs>
72 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
73 <param name="samFile" type="data" format="sam,bam"/>
74 </repeat>
75
76 <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
77 help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
78 bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
79
80 <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp"
81 help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
82 Otherwise all reads in the interval are considered. " argument="--binSize"/>
83
84 <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
85 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
86 (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>
87
88 <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
89 help="Restriction sites that are closer that this distance are merged into one.
90 This option only applies if --restrictionCutFile is given." argument="--minDistance"/>
91
92 <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
93 help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/>
94
95 <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
96 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
97 &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>
98
99 <expand macro="region" />
100
101 <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue=""
102 label="Save the matrix of values underlying the heatmap" help="If set, outward facing reads, at a distance of less thatn 25kbs are removed." />
103
104 <expand macro="minMappingQuality" />
105
106 </inputs>
107 <outputs>
108 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
109 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
110 <data name="qc" format="html" label="${tool.name} QC"/>
111 </outputs>
112 <tests>
113 <test>
114 <repeat name="samFiles">
115 <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
116 </repeat>
117 <repeat name="samFiles">
118 <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
119 </repeat>
120 <param name="binSize" value="5000"/>
121 <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/>
122 <output name="outFileName" file="hicBuildMatrix_result1.h5" ftype="h5" compare="sim_size"/>
123 </test>
124 </tests>
125 <help><![CDATA[
126
127 **What it does**
128
129 Creates a matrix of interactions.
130
131 ]]></help>
132 <expand macro="citations" />
133 </tool>