Mercurial > repos > bgruening > hicexplorer_hicquickqc
comparison hicQuickQC.xml @ 6:9c5078f3926b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author | iuc |
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date | Tue, 16 Mar 2021 15:08:31 +0000 |
parents | 909125ec301f |
children | 21d859ad4502 |
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5:b8755bb5bc56 | 6:9c5078f3926b |
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1 <tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
2 <description>get a first quality estimate of Hi-C data</description> | 2 <description>get a first quality estimate of Hi-C data</description> |
3 <macros> | 3 <macros> |
4 <token name="@BINARY@">hicQuickQC</token> | 4 <token name="@BINARY@">hicQuickQC</token> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
14 --samFiles | 14 --samFiles |
15 #for $repeat in $samFiles: | 15 #for $repeat in $samFiles: |
16 '${repeat.samFile}' | 16 '${repeat.samFile}' |
17 #end for | 17 #end for |
18 | 18 |
19 --restrictionCutFile '$restrictionCutFile' | |
20 | |
19 #if $restrictionSequence: | 21 #if $restrictionSequence: |
20 --restrictionSequence '$restrictionSequence' | 22 --restrictionSequence '$restrictionSequence' |
21 #end if | 23 #end if |
22 | 24 |
23 #if $danglingSequence: | 25 #if $danglingSequence: |
28 --lines $lines | 30 --lines $lines |
29 | 31 |
30 && mv ./QCfolder/* $qc.files_path/ | 32 && mv ./QCfolder/* $qc.files_path/ |
31 && mv $qc.files_path/hicQC.html $qc | 33 && mv $qc.files_path/hicQC.html $qc |
32 && mv $qc.files_path/*.log raw_qc | 34 && mv $qc.files_path/*.log raw_qc |
33 ]]></command> | 35 ]]> </command> |
34 <inputs> | 36 <inputs> |
35 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" | 37 <!-- can we use multiple="true" with min="2" and max="2" ? --> |
36 help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> | 38 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> |
37 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/> | 39 <param name="samFile" type="data" format="sam,qname_input_sorted.bam" /> |
38 </repeat> | 40 </repeat> |
41 <expand macro="restrictionCutFile" /> | |
42 <expand macro="restrictionSequence" /> | |
43 <expand macro="danglingSequence" /> | |
39 | 44 |
40 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" | 45 <param argument="--lines" optional='true' type="integer" label="Lines to analyze for the QC report" help= "Number of lines to consider for the qc test run." value='1000000' /> |
41 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or | |
42 "dangling-ends". If not given, such statistics will not be available." /> | |
43 | |
44 <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence" | |
45 help="Sequence left by the restriction enzyme after cutting. | |
46 Each restriction enzyme recognizes a different DNA sequence and, | |
47 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence. | |
48 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. | |
49 For DpnII, the restriction site and dangling end sequence are the same: GATC. | |
50 This information is easily found on the description of the restriction enzyme. | |
51 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. | |
52 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/> | |
53 | |
54 <param argument="--lines" optional='true' type="integer" label="Lines" help= "Number of lines to consider for the qc test run." value='1000000'/> | |
55 | 46 |
56 </inputs> | 47 </inputs> |
57 <outputs> | 48 <outputs> |
58 <data name="qc" format="html" label="${tool.name} QC on ${on_string}"/> | 49 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> |
59 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" /> | 50 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" /> |
60 </outputs> | 51 </outputs> |
61 <tests> | 52 <tests> |
62 <test> | 53 <test expect_num_outputs="2"> |
63 <repeat name="samFiles"> | 54 <repeat name="samFiles"> |
64 <param name="samFile" value="small_test_R1_unsorted.sam"/> | 55 <param name="samFile" value="small_test_R1_unsorted.sam" /> |
65 </repeat> | 56 </repeat> |
66 <repeat name="samFiles"> | 57 <repeat name="samFiles"> |
67 <param name="samFile" value="small_test_R2_unsorted.sam"/> | 58 <param name="samFile" value="small_test_R2_unsorted.sam" /> |
68 </repeat> | 59 </repeat> |
69 <conditional name="restrictionCutFileBinSize_conditional"> | 60 <param name='restrictionCutFile' value='DpnII_10k.bed' /> |
70 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/> | 61 <param name='restrictionSequence' value='GATC' /> |
71 <repeat name='binSizes'> | 62 <param name='danglingSequence' value='GATC' /> |
72 <param name="binSize" value="5000"/> | 63 |
73 </repeat> | 64 <param name="lines" value='1000' /> |
74 </conditional> | 65 <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2' /> |
75 <param name="lines" value='1000'/> | |
76 <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2'/> | |
77 </test> | 66 </test> |
78 </tests> | 67 </tests> |
79 <help><![CDATA[ | 68 <help><![CDATA[ |
80 | 69 |
81 Quick QC | 70 Quick QC |
82 ==================== | 71 ======== |
83 | 72 |
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. | 73 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. |
85 | 74 |
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. | 75 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. |
87 | 76 |
88 For more information about HiCExplorer please consider our documentation on readthedocs.io_ | 77 For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
89 | 78 |
90 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 79 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
91 ]]></help> | 80 ]]> </help> |
92 <expand macro="citations" /> | 81 <expand macro="citations" /> |
93 </tool> | 82 </tool> |