Mercurial > repos > bgruening > hicexplorer_hicquickqc

comparison 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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-1:000000000000 0:269c4246279d
1 <tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>get a first quality estimate of Hi-C data</description>
3 <macros>
4 <token name="@BINARY@">hicQuickQC</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 mkdir ./QCfolder &&
11 mkdir $qc.files_path &&
12 @BINARY@
13
14 --samFiles
15 #for $repeat in $samFiles:
16 '${repeat.samFile}'
17 #end for
18
19 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
20 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
21 --minDistance $restrictionCutFileBinSize_conditional.minDistance
22 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
23 #end if
24
25 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
26 --binSize
27 #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
28 '${repeat.binSize}'
29 #end for
30 #end if
31
32
33 #if $restrictionSequence:
34 --restrictionSequence '$restrictionSequence'
35 #end if
36
37 #if $danglingSequence:
38 --danglingSequence '$danglingSequence'
39 #end if
40 --QCfolder ./QCfolder
41
42 --lines $lines
43
44 && mv ./QCfolder/* $qc.files_path/
45 && mv $qc.files_path/hicQC.html $qc
46 && mv $qc.files_path/*.log raw_qc
47 ]]></command>
48 <inputs>
49 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
50 help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
51 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
52 </repeat>
53 <conditional name="restrictionCutFileBinSize_conditional">
54 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
55 <option value="optionRestrictionCutFile">Restriction cut file</option>
56 <option value="optionBinSize" selected="True">Bin size</option>
57 </param>
58 <when value="optionRestrictionCutFile">
59 <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
60 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
61 (i.e. the region between one restriction site and the next)." />
62 <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
63 help="Restriction sites that are closer that this distance are merged into one.
64 This option only applies if --restrictionCutFile is given."/>
65 <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
66 label="Maximum library insert size defines different cut offs based on the maximum expected library size"
67 help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
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
69 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
70 is too far away from the nearest restriction site." />
71 </when>
72 <when value="optionBinSize">
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.
74 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
75 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/>
76 </repeat>
77 </when>
78 </conditional>
79
80 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
81 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
82 &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
83
84 <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
85 help="Sequence left by the restriction enzyme after cutting.
86 Each restriction enzyme recognizes a different DNA sequence and,
87 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
88 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
89 For DpnII, the restriction site and dangling end sequence are the same: GATC.
90 This information is easily found on the description of the restriction enzyme.
91 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
92 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>
93
94 <param argument="--lines" optional='true' type="integer" label="Lines" help= "Number of lines to consider for the qc test run." value='1000000'/>
95
96 </inputs>
97 <outputs>
98 <data name="qc" format="html" label="${tool.name} QC on ${on_string}"/>
99 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
100 </outputs>
101 <tests>
102 <test>
103 <repeat name="samFiles">
104 <param name="samFile" value="small_test_R1_unsorted.sam"/>
105 </repeat>
106 <repeat name="samFiles">
107 <param name="samFile" value="small_test_R2_unsorted.sam"/>
108 </repeat>
109 <conditional name="restrictionCutFileBinSize_conditional">
110 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
111 <repeat name='binSizes'>
112 <param name="binSize" value="5000"/>
113 </repeat>
114 </conditional>
115 <param name="lines" value='1000'/>
116 <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2'/>
117 </test>
118 </tests>
119 <help><![CDATA[
120
121 Quick QC
122 ====================
123
124 Get a quick impression on the quality of your Hi-C data. The first
125
126 For more information about HiCExplorer please consider our documentation on readthedocs.io_
127
128 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
129 ]]></help>
130 <expand macro="citations" />
131 </tool>