Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 22:a4c13ddcc8ee draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:52:43 +0000
parents ed2cca6b5de4
children
comparison
equal deleted inserted replaced
21:ed2cca6b5de4 22:a4c13ddcc8ee
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="1.9">samtools</requirement> 8 <requirement type="package" version="1.19">samtools</requirement>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 11
12 mkdir ./QCfolder && 12 mkdir ./QCfolder &&
13 mkdir '$qc.files_path' && 13 mkdir '$qc.files_path' &&
16 #for $repeat in $samFiles: 16 #for $repeat in $samFiles:
17 '${repeat.samFile}' 17 '${repeat.samFile}'
18 #end for 18 #end for
19 19
20 --restrictionCutFile '$restrictionCutFile' 20 --restrictionCutFile '$restrictionCutFile'
21 21
22 #if $restrictionSequence: 22 #if $restrictionSequence:
23 --restrictionSequence '$restrictionSequence' 23 --restrictionSequence '$restrictionSequence'
24 #end if 24 #end if
25 #if $danglingSequence: 25 #if $danglingSequence:
26 --danglingSequence '$danglingSequence' 26 --danglingSequence '$danglingSequence'
29 --minDistance $minDistance 29 --minDistance $minDistance
30 #end if 30 #end if
31 #if $maxLibraryInsertSize: 31 #if $maxLibraryInsertSize:
32 --maxLibraryInsertSize $maxLibraryInsertSize 32 --maxLibraryInsertSize $maxLibraryInsertSize
33 #end if 33 #end if
34 34
35 #if $binSizes: 35 #if $binSizes:
36 --binSize 36 --binSize
37 #for $repeat in $binSizes 37 #for $repeat in $binSizes
38 '${repeat.binSize}' 38 '${repeat.binSize}'
39 #end for 39 #end for
40 #end if 40 #end if
41 41
42 --genomeAssembly $samFiles[0].samFile.metadata.dbkey 42 #if $chromosomeSizes:
43 --chromosomeSizes '$chromosomeSizes'
44 #end if
45 #if $dbKey:
46 --genomeAssembly '$dbKey'
47 #else
48 --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
49 #end if
43 50
44 #if $region: 51 #if $region:
45 --region '$region' 52 --region '$region'
46 #end if 53 #end if
47 54
48 --outFileName matrix.$outputFormat 55 --outFileName 'matrix.$outputFormat'
49 56
50 #if $outBam: 57 #if $outBam:
51 $outBam ./unsorted.bam 58 $outBam ./unsorted.bam
52 #end if 59 #end if
53 60
55 $keepSelfLigation 62 $keepSelfLigation
56 $skipDuplicationCheck 63 $skipDuplicationCheck
57 64
58 #if $minMappingQuality and $minMappingQuality is not None: 65 #if $minMappingQuality and $minMappingQuality is not None:
59 --minMappingQuality $minMappingQuality 66 --minMappingQuality $minMappingQuality
60 #end if
61
62 #if $chromosomeSizes:
63 --chromosomeSizes '$chromosomeSizes'
64 #end if 67 #end if
65 68
66 --threads @THREADS@ 69 --threads @THREADS@
67 70
68 --QCfolder ./QCfolder 71 --QCfolder ./QCfolder
79 </command> 82 </command>
80 <inputs> 83 <inputs>
81 <!-- can we use multiple=True here with min="2" and max="2" ? --> 84 <!-- can we use multiple=True here with min="2" and max="2" ? -->
82 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> 85 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
83 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"> 86 <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
84 <validator type="unspecified_build" />
85 </param> 87 </param>
86 </repeat> 88 </repeat>
87 89
88 <expand macro="restrictionCutFile" /> 90 <expand macro="restrictionCutFile" />
89 <expand macro="restrictionSequence" /> 91 <expand macro="restrictionSequence" />
105 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." /> 107 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
106 <param argument="--keepSelfLigation" type="boolean" truevalue="--keepSelfLigation" falsevalue="" label="Keep self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are kept. Although this reads do not contribute to any distant contact, they are useful to account for bias in the data." /> 108 <param argument="--keepSelfLigation" type="boolean" truevalue="--keepSelfLigation" falsevalue="" label="Keep self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are kept. Although this reads do not contribute to any distant contact, they are useful to account for bias in the data." />
107 <expand macro="minMappingQuality" /> 109 <expand macro="minMappingQuality" />
108 <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." /> 110 <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." />
109 <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected 111 <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected
110 Usually the sizes can be determined from the SAM/BAM input files, however, 112 Usually the sizes can be determined from the SAM/BAM input files, however,
111 for cHi-C or scHi-C it can be that at the start or end no data is present. 113 for cHi-C or scHi-C it can be that at the start or end no data is present.
112 Please consider that this option causes that only reads are considered which are on the listed chromosomes. 114 Please consider that this option causes that only reads are considered which are on the listed chromosomes.
113 Use this option to guarantee fixed sizes. An example file is available via UCSC: 115 Use this option to guarantee fixed sizes. An example file is available via UCSC:
114 http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" /> 116 http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" />
117 <param name="dbKey" type="text" optional="true" label="Use this dbkey for your history genome"
118 help="You can set the reference genome in your history as metadata. In case you have not you can specify it here." />
115 119
116 <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam 120 <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam
117 file containing all valid Hi-C reads can be created 121 file containing all valid Hi-C reads can be created
118 using this option. This bam file could be useful to 122 using this option. This bam file could be useful to
119 inspect the distribution of valid Hi-C reads pairs or 123 inspect the distribution of valid Hi-C reads pairs or
152 </repeat> 156 </repeat>
153 <param name="restrictionCutFile" value="DpnII_10k.bed" /> 157 <param name="restrictionCutFile" value="DpnII_10k.bed" />
154 <param name="restrictionSequence" value="GATC" /> 158 <param name="restrictionSequence" value="GATC" />
155 <param name="danglingSequence" value="GATC" /> 159 <param name="danglingSequence" value="GATC" />
156 <param name="outBam" value="True" /> 160 <param name="outBam" value="True" />
157 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" /> 161 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" />
158 <output name="outFileName" ftype="h5"> 162 <output name="outFileName" ftype="h5">
159 <assert_contents> 163 <assert_contents>
160 <has_h5_keys keys="intervals,matrix" /> 164 <has_h5_keys keys="intervals,matrix" />
161 </assert_contents> 165 </assert_contents>
162 </output> 166 </output>
175 <param name="restrictionCutFile" value="DpnII_10k.bed" /> 179 <param name="restrictionCutFile" value="DpnII_10k.bed" />
176 <param name="restrictionSequence" value="GATC" /> 180 <param name="restrictionSequence" value="GATC" />
177 <param name="danglingSequence" value="GATC" /> 181 <param name="danglingSequence" value="GATC" />
178 <param name="outputFormat" value="cool" /> 182 <param name="outputFormat" value="cool" />
179 <param name="outBam" value="True" /> 183 <param name="outBam" value="True" />
180 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" /> 184 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" />
181 <output name="outFileName" ftype="cool"> 185 <output name="outFileName" ftype="cool">
182 <assert_contents> 186 <assert_contents>
183 <has_h5_keys keys="bins,chroms,indexes,pixels" /> 187 <has_h5_keys keys="bins,chroms,indexes,pixels" />
184 </assert_contents> 188 </assert_contents>
185 </output> 189 </output>