Mercurial > repos > bgruening > hicexplorer_hicquickqc

annotate hicQuickQC.xml @ 0:269c4246279d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:38:29 -0500
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children b599d3000966
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1 <tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>get a first quality estimate of Hi-C data</description>
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3 <macros>
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4 <token name="@BINARY@">hicQuickQC</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 detect_errors="exit_code"><![CDATA[
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9
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10 mkdir ./QCfolder &&
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11 mkdir $qc.files_path &&
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12 @BINARY@
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13
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14 --samFiles
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15 #for $repeat in $samFiles:
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16 '${repeat.samFile}'
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17 #end for
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18
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19 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
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20 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
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21 --minDistance $restrictionCutFileBinSize_conditional.minDistance
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22 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
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23 #end if
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25 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
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26 --binSize
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27 #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
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28 '${repeat.binSize}'
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29 #end for
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30 #end if
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33 #if $restrictionSequence:
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34 --restrictionSequence '$restrictionSequence'
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35 #end if
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36
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37 #if $danglingSequence:
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38 --danglingSequence '$danglingSequence'
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39 #end if
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40 --QCfolder ./QCfolder
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41
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42 --lines $lines
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43
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44 && mv ./QCfolder/* $qc.files_path/
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45 && mv $qc.files_path/hicQC.html $qc
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46 && mv $qc.files_path/*.log raw_qc
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47 ]]></command>
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48 <inputs>
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49 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
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50 help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
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51 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
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52 </repeat>
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53 <conditional name="restrictionCutFileBinSize_conditional">
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54 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
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55 <option value="optionRestrictionCutFile">Restriction cut file</option>
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56 <option value="optionBinSize" selected="True">Bin size</option>
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57 </param>
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58 <when value="optionRestrictionCutFile">
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59 <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
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60 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
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61 (i.e. the region between one restriction site and the next)." />
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62 <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
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63 help="Restriction sites that are closer that this distance are merged into one.
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64 This option only applies if --restrictionCutFile is given."/>
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65 <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
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66 label="Maximum library insert size defines different cut offs based on the maximum expected library size"
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67 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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68 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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69 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
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70 is too far away from the nearest restriction site." />
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71 </when>
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72 <when value="optionBinSize">
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73 <repeat name='binSizes' title='Bin size in bp' min="1" 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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74 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
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75 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/>
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76 </repeat>
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77 </when>
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78 </conditional>
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79
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80 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
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81 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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82 &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
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83
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84 <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
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85 help="Sequence left by the restriction enzyme after cutting.
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86 Each restriction enzyme recognizes a different DNA sequence and,
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87 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
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88 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
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89 For DpnII, the restriction site and dangling end sequence are the same: GATC.
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90 This information is easily found on the description of the restriction enzyme.
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91 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
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92 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>
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93
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94 <param argument="--lines" optional='true' type="integer" label="Lines" help= "Number of lines to consider for the qc test run." value='1000000'/>
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95
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96 </inputs>
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97 <outputs>
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98 <data name="qc" format="html" label="${tool.name} QC on ${on_string}"/>
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99 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
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100 </outputs>
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101 <tests>
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102 <test>
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103 <repeat name="samFiles">
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104 <param name="samFile" value="small_test_R1_unsorted.sam"/>
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105 </repeat>
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106 <repeat name="samFiles">
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107 <param name="samFile" value="small_test_R2_unsorted.sam"/>
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108 </repeat>
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109 <conditional name="restrictionCutFileBinSize_conditional">
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110 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
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111 <repeat name='binSizes'>
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112 <param name="binSize" value="5000"/>
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113 </repeat>
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114 </conditional>
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115 <param name="lines" value='1000'/>
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116 <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2'/>
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120
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121 Quick QC
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122 ====================
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123
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124 Get a quick impression on the quality of your Hi-C data. The first
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125
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126 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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127
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128 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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129 ]]></help>
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130 <expand macro="citations" />
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131 </tool>