Mercurial > repos > bgruening > hicexplorer_hicquickqc

annotate hicQuickQC.xml @ 5:b8755bb5bc56 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author iuc
date Fri, 11 Dec 2020 21:05:59 +0000
parents 909125ec301f
children 9c5078f3926b
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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
0
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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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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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19 #if $restrictionSequence:
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20 --restrictionSequence '$restrictionSequence'
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21 #end if
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22
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23 #if $danglingSequence:
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24 --danglingSequence '$danglingSequence'
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25 #end if
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26 --QCfolder ./QCfolder
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28 --lines $lines
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30 && mv ./QCfolder/* $qc.files_path/
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31 && mv $qc.files_path/hicQC.html $qc
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32 && mv $qc.files_path/*.log raw_qc
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33 ]]></command>
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34 <inputs>
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35 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
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36 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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37 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
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38 </repeat>
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39
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40 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
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41 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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42 &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
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43
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44 <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
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45 help="Sequence left by the restriction enzyme after cutting.
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46 Each restriction enzyme recognizes a different DNA sequence and,
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47 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
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48 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
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49 For DpnII, the restriction site and dangling end sequence are the same: GATC.
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50 This information is easily found on the description of the restriction enzyme.
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51 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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52 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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53
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54 <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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55
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56 </inputs>
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57 <outputs>
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58 <data name="qc" format="html" label="${tool.name} QC on ${on_string}"/>
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59 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <repeat name="samFiles">
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64 <param name="samFile" value="small_test_R1_unsorted.sam"/>
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65 </repeat>
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66 <repeat name="samFiles">
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67 <param name="samFile" value="small_test_R2_unsorted.sam"/>
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68 </repeat>
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69 <conditional name="restrictionCutFileBinSize_conditional">
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70 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
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71 <repeat name='binSizes'>
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72 <param name="binSize" value="5000"/>
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73 </repeat>
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74 </conditional>
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75 <param name="lines" value='1000'/>
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76 <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2'/>
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77 </test>
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78 </tests>
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79 <help><![CDATA[
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80
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81 Quick QC
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82 ====================
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83
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84 Get a quick impression on the quality of your Hi-C data. hicQuickQC considers the first n lines of two bam/sam files to get a first estimate of the quality of the data. It is highly recommended to set the restriction enzyme and dangling end parameter to get a good quality report.
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85
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86 The default is to read the first 1,000,000 reads of the mapped bam files to get a quality estimate of the Hi-C data.
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88 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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90 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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91 ]]></help>
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92 <expand macro="citations" />
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93 </tool>