Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

annotate hicBuildMatrix.xml @ 3:2a13bfe5bff2 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
author iuc
date Mon, 27 Nov 2017 11:15:32 -0500
parents eb0d14cdf8b8
children 652fdcbff650
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>creates a matrix of interactions</description>
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3 <macros>
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4 <token name="@BINARY@">hicBuildMatrix</token>
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5 <import>macros.xml</import>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 </macros>
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7 <expand macro="requirements" >
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8 <requirement type="package" version="1.6">samtools</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 mkdir ./QCfolder &&
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13 mkdir $qc.files_path &&
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 hicBuildMatrix
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16 --samFiles
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17 #for $repeat in $samFiles:
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18 '${repeat.samFile}'
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19 #end for
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20
2
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21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
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22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
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23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
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24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
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25 #end if
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27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
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28 --binSize $restrictionCutFileBinSize_conditional.binSize
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29 #end if
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 #if $restrictionSequence:
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33 --restrictionSequence '$restrictionSequence'
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34 #end if
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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36 #if $region:
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37 --region '$region'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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38 #end if
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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40 --outFileName ./matrix.h5
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 --outBam ./unsorted.bam
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42
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43 $keepSelfCircles
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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45 #if $minMappingQuality and $minMappingQuality is not None:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 --minMappingQuality $minMappingQuality
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47 #end if
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48
2
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49 #if $danglingSequence:
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50 --danglingSequence '$danglingSequence'
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51 #end if
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52
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53 --threads @THREADS@
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54
0
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55 --QCfolder ./QCfolder
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56 &&
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57 mv ./QCfolder/* $qc.files_path/
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58 &&
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59 mv $qc.files_path/hicQC.html $qc
2
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60 && samtools sort ./unsorted.bam -o sorted.bam
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61
0
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62 ]]>
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63 </command>
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64 <inputs>
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65 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
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66 <param name="samFile" type="data" format="sam,bam"/>
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67 </repeat>
2
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68 <conditional name="restrictionCutFileBinSize_conditional">
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69 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
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70 <option value="optionRestrictionCutFile">Restriction cut file</option>
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71 <option value="optionBinSize" selected="True">Bin size</option>
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72 </param>
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73 <when value="optionRestrictionCutFile">
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74 <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
2
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75 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
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76 (i.e. the region between one restriction site and the next)." />
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77 <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
2
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78 help="Restriction sites that are closer that this distance are merged into one.
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79 This option only applies if --restrictionCutFile is given."/>
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80 <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
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81 label="Maximum library insert size defines different cut offs based on the maximum expected library size"
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82 help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
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83 which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
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84 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
2a13bfe5bff2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
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85 is too far away from the nearest restriction site." />
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86 </when>
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87 <when value="optionBinSize">
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88 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"
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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.
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90 Otherwise all reads in the interval are considered. "/>
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91 </when>
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92 </conditional>
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93
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94 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
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95 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
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96 &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
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97
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98 <expand macro="region" />
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99
2
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100 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue=""
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101 label="Keep self circles"
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102 help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
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103
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104 <expand macro="minMappingQuality" />
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105
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106 <param argument="--danglingSequence" type="text" optional="true" label="The dangling sequence"
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107 help="Dangling end sequence left by the restriction enzyme. For DpnII for example,
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108 the dangling end is the same restriction sequence. This is used
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109 to discard reads that end/start with such sequence
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110 and that are considered un-ligated fragments or
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111 'dangling-ends'. If not given, such statistics will
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112 not be available."/>
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113 </inputs>
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114 <outputs>
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115 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
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116 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
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117 <data name="qc" format="html" label="${tool.name} QC"/>
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118 </outputs>
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119 <tests>
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120 <test>
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121 <repeat name="samFiles">
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122 <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
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123 </repeat>
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124 <repeat name="samFiles">
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125 <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
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126 </repeat>
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127 <conditional name="restrictionCutFileBinSize_conditional">
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128 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
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129 <param name="binSize" value="5000"/>
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130 </conditional>
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131 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
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132 <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136
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137 **What it does**
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138
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139 Creates a matrix of interactions.
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140
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141 ]]></help>
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142 <expand macro="citations" />
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143 </tool>