Mercurial > repos > bgruening > hicexplorer_hicquickqc

comparison hicQuickQC.xml @ 8:21d859ad4502 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:11:51 +0000
parents 9c5078f3926b
children ea8fb5e899e8
comparison
equal deleted inserted replaced
7:7679948176ef 8:21d859ad4502
39 <param name="samFile" type="data" format="sam,qname_input_sorted.bam" /> 39 <param name="samFile" type="data" format="sam,qname_input_sorted.bam" />
40 </repeat> 40 </repeat>
41 <expand macro="restrictionCutFile" /> 41 <expand macro="restrictionCutFile" />
42 <expand macro="restrictionSequence" /> 42 <expand macro="restrictionSequence" />
43 <expand macro="danglingSequence" /> 43 <expand macro="danglingSequence" />
44 44 <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" />
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' />
46
47 </inputs> 45 </inputs>
48 <outputs> 46 <outputs>
49 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> 47 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
50 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" /> 48 <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" />
51 </outputs> 49 </outputs>
52 <tests> 50 <tests>
53 <test expect_num_outputs="2"> 51 <test expect_num_outputs="2">
54 <repeat name="samFiles"> 52 <repeat name="samFiles">
55 <param name="samFile" value="small_test_R1_unsorted.sam" /> 53 <param name="samFile" value="small_test_R1_unsorted.sam" />
56 </repeat> 54 </repeat>
57 <repeat name="samFiles"> 55 <repeat name="samFiles">
58 <param name="samFile" value="small_test_R2_unsorted.sam" /> 56 <param name="samFile" value="small_test_R2_unsorted.sam" />
59 </repeat> 57 </repeat>
60 <param name='restrictionCutFile' value='DpnII_10k.bed' /> 58 <param name="restrictionCutFile" value="DpnII_10k.bed" />
61 <param name='restrictionSequence' value='GATC' /> 59 <param name="restrictionSequence" value="GATC" />
62 <param name='danglingSequence' value='GATC' /> 60 <param name="danglingSequence" value="GATC" />
63 61 <param name="lines" value="1000" />
64 <param name="lines" value='1000' /> 62 <output name="raw_qc" file="hicQuickQC/QC.log" compare="diff" lines_diff="2" />
65 <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2' />
66 </test> 63 </test>
67 </tests> 64 </tests>
68 <help><![CDATA[ 65 <help><![CDATA[
69 66
70 Quick QC 67 Quick QC