Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

annotate hicBuildMatrix.xml @ 0:611b0f02e109 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
author bgruening
date Sun, 09 Oct 2016 17:35:32 -0400
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611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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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>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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11 hicBuildMatrix
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12
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13 --samFiles
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14 #for $repeat in $samFiles:
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15 '${repeat.samFile}'
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16 #end for
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17
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18 #if $binSize and $binSize is not None:
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19 --binSize $binSize
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20 #end if
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21
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22 #if $fragmentLength and $fragmentLength is not None:
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23 --fragmentLength $fragmentLength
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24 #end if
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25
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26 #if $restrictionCutFile and $restrictionCutFile is not None:
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27 --restrictionCutFile $restrictionCutFile
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28 #end if
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29
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30 #if $minDistance and $minDistance is not None:
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31 --minDistance $minDistance
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32 #end if
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33
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34 #if $maxDistance and $maxDistance is not None:
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35 --maxDistance $maxDistance
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36 #end if
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37
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38 #if $restrictionSequence and $restrictionSequence is not None:
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39 --restrictionSequence '$restrictionSequence'
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40 #end if
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41
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42 #if $region and $region is not None:
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43 --region '$region'
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44 #end if
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45
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46 --outFileName ./numpy_array.npz
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47 --outBam ./unsorted.bam
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48
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49 #if $restrictionCutFile:
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50 --restrictionCutFile '$restrictionCutFile'
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51 #end if
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52
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53 $removeSelfCircles
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54
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55 #if $minMappingQuality
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56 --minMappingQuality $minMappingQuality
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57 #end if
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58 &&
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59
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60 samtools sort ./unsorted.bam -o sorted.bam
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61
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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>
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68
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69 <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
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70 help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
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71 bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
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72
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73 <param name="binSize" type="integer" value="10000" label="Bin size in bp"
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74 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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75 Otherwise all reads in the interval are considered. " argument="--binSize"/>
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76
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77 <param name="fragmentLength" type="integer" value="300" optional="true" label="Estimated fragment length" argument="--fragmentLength" />
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78
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79 <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
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80 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
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81 (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>
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82
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83 <param name="minDistance" type="integer" value="300" optional="true" label="Minimum distance between restriction sites"
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84 help="Restriction sites that are closer that this distance are merged into one.
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85 This option only applies if --restrictionCutFile is given." argument="--minDistance"/>
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86
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87 <param name="maxDistance" type="integer" value="800" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
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88 help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/>
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89
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90 <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
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91 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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92 &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>
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93
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94 <expand macro="region" />
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95
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96 <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue=""
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97 label="Save the matrix of values underlying the heatmap" help="If set, outward facing reads, at a distance of less thatn 25kbs are removed." />
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98
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99 <expand macro="minMappingQuality" />
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100
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101
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102 </inputs>
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103 <outputs>
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104 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
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105 <data name="outFileName" from_work_dir="numpy_array.npz.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
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106 </outputs>
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107 <tests>
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108 <test>
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109 <repeat name="samFiles">
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110 <param name="samFile" value="r1.sam" ftype="sam" />
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111 </repeat>
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112 <repeat name="samFiles">
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113 <param name="samFile" value="r2.sam" ftype="sam"/>
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114 </repeat>
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115 <param name="binSize" value="10000"/>
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116 <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/>
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117 <output name="outFileName" file="hicBuildMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
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118 </test>
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119 </tests>
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120 <help><![CDATA[
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121
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122 **What it does**
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123
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124 Creates a matrix of interactions
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125
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126 ]]></help>
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127 <expand macro="citations" />
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128 </tool>