Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 2:eb0d14cdf8b8 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:11:01 -0400
parents 9767c021cd58
children 2a13bfe5bff2
comparison
equal deleted inserted replaced
1:3d56e784d0bd 2:eb0d14cdf8b8
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicBuildMatrix</token> 4 <token name="@BINARY@">hicBuildMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" > 7 <expand macro="requirements" >
8 <requirement type="package" version="1.3.1">samtools</requirement> 8 <requirement type="package" version="1.6">samtools</requirement>
9 </expand> 9 </expand>
10 <command> 10 <command detect_errors="exit_code"><![CDATA[
11 <![CDATA[
12 11
13 mkdir ./QCfolder && 12 mkdir ./QCfolder &&
14 mkdir $qc.files_path 13 mkdir $qc.files_path &&
15 &&
16
17 hicBuildMatrix 14 hicBuildMatrix
18 15
19 --samFiles 16 --samFiles
20 #for $repeat in $samFiles: 17 #for $repeat in $samFiles:
21 '${repeat.samFile}' 18 '${repeat.samFile}'
22 #end for 19 #end for
23 20
24 #if $binSize: 21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
25 --binSize $binSize 22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
24 --maxDistance $restrictionCutFileBinSize_conditional.maxDistance
26 #end if 25 #end if
27 26
28 #if $restrictionCutFile: 27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
29 --restrictionCutFile '$restrictionCutFile' 28 --binSize $restrictionCutFileBinSize_conditional.binSize
30 #end if 29 #end if
31 30
32 #if $minDistance:
33 --minDistance $minDistance
34 #end if
35
36 #if $maxDistance:
37 --maxDistance $maxDistance
38 #end if
39 31
40 #if $restrictionSequence: 32 #if $restrictionSequence:
41 --restrictionSequence '$restrictionSequence' 33 --restrictionSequence '$restrictionSequence'
42 #end if 34 #end if
43 35
46 #end if 38 #end if
47 39
48 --outFileName ./matrix.h5 40 --outFileName ./matrix.h5
49 --outBam ./unsorted.bam 41 --outBam ./unsorted.bam
50 42
51 #if $restrictionCutFile: 43 $keepSelfCircles
52 --restrictionCutFile '$restrictionCutFile'
53 #end if
54
55 $removeSelfCircles
56 44
57 #if $minMappingQuality and $minMappingQuality is not None: 45 #if $minMappingQuality and $minMappingQuality is not None:
58 --minMappingQuality $minMappingQuality 46 --minMappingQuality $minMappingQuality
59 #end if 47 #end if
60 48
49 #if $danglingSequence:
50 --danglingSequence '$danglingSequence'
51 #end if
52
53 --threads @THREADS@
54
61 --QCfolder ./QCfolder 55 --QCfolder ./QCfolder
62 && 56 &&
63 mv ./QCfolder/* $qc.files_path/ 57 mv ./QCfolder/* $qc.files_path/
64 && 58 &&
65 mv $qc.files_path/hicQC.html $qc 59 mv $qc.files_path/hicQC.html $qc
66 && 60 && samtools sort ./unsorted.bam -o sorted.bam
67 samtools sort ./unsorted.bam -o sorted.bam 61
68
69 ]]> 62 ]]>
70 </command> 63 </command>
71 <inputs> 64 <inputs>
72 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process"> 65 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
73 <param name="samFile" type="data" format="sam,bam"/> 66 <param name="samFile" type="data" format="sam,bam"/>
74 </repeat> 67 </repeat>
68 <conditional name="restrictionCutFileBinSize_conditional">
69 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
70 <option value="optionRestrictionCutFile">Restriction cut file</option>
71 <option value="optionBinSize" selected="True">Bin size</option>
72 </param>
73 <when value="optionRestrictionCutFile">
74 <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
75 help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
76 bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
77 <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
78 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
79 (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>
80 <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
81 help="Restriction sites that are closer that this distance are merged into one.
82 This option only applies if --restrictionCutFile is given." argument="--minDistance"/>
75 83
76 <param argument="--restrictionCutFile" type="data" format="bed" optional="True" 84 <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"
77 help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the 85 help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/>
78 bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/> 86 </when>
79 87 <when value="optionBinSize">
80 <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp" 88 <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. 89 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"/> 90 Otherwise all reads in the interval are considered. " argument="--binSize"/>
83 91 </when>
84 <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places" 92 </conditional>
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 93
95 <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" 94 <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 95 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"/> 96 &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>
98 97
99 <expand macro="region" /> 98 <expand macro="region" />
100 99
101 <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue="" 100 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" 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." /> 101 label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. '
102 + 'They will be counted and shown in the QC plots." />
103 103
104 <expand macro="minMappingQuality" /> 104 <expand macro="minMappingQuality" />
105 105
106 <param name="danglingSequence" type="text" optional="true" label="The dangling sequence"
107 help="Dangling end sequence left by the restriction enzyme. For DpnII for example,
108 the dangling end is the same restriction sequence. This is used
109 to discard reads that end/start with such sequence
110 and that are considered un-ligated fragments or
111 'dangling-ends'. If not given, such statistics will
112 not be available." argument="--danglingSequence"/>
106 </inputs> 113 </inputs>
107 <outputs> 114 <outputs>
108 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/> 115 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
109 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/> 116 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
110 <data name="qc" format="html" label="${tool.name} QC"/> 117 <data name="qc" format="html" label="${tool.name} QC"/>
115 <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" /> 122 <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
116 </repeat> 123 </repeat>
117 <repeat name="samFiles"> 124 <repeat name="samFiles">
118 <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/> 125 <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
119 </repeat> 126 </repeat>
120 <param name="binSize" value="5000"/> 127 <conditional name="restrictionCutFileBinSize_conditional">
121 <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/> 128 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
122 <output name="outFileName" file="hicBuildMatrix_result1.h5" ftype="h5" compare="sim_size"/> 129 <param name="binSize" value="5000"/>
130 </conditional>
131 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
132 <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
123 </test> 133 </test>
124 </tests> 134 </tests>
125 <help><![CDATA[ 135 <help><![CDATA[
126 136
127 **What it does** 137 **What it does**