Mercurial > repos > bgruening > hicexplorer_hicquickqc
view hicQuickQC.xml @ 6:9c5078f3926b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author | iuc |
---|---|
date | Tue, 16 Mar 2021 15:08:31 +0000 |
parents | 909125ec301f |
children | 21d859ad4502 |
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<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>get a first quality estimate of Hi-C data</description> <macros> <token name="@BINARY@">hicQuickQC</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ mkdir ./QCfolder && mkdir $qc.files_path && @BINARY@ --samFiles #for $repeat in $samFiles: '${repeat.samFile}' #end for --restrictionCutFile '$restrictionCutFile' #if $restrictionSequence: --restrictionSequence '$restrictionSequence' #end if #if $danglingSequence: --danglingSequence '$danglingSequence' #end if --QCfolder ./QCfolder --lines $lines && mv ./QCfolder/* $qc.files_path/ && mv $qc.files_path/hicQC.html $qc && mv $qc.files_path/*.log raw_qc ]]> </command> <inputs> <!-- can we use multiple="true" with min="2" and max="2" ? --> <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> <param name="samFile" type="data" format="sam,qname_input_sorted.bam" /> </repeat> <expand macro="restrictionCutFile" /> <expand macro="restrictionSequence" /> <expand macro="danglingSequence" /> <param argument="--lines" optional='true' type="integer" label="Lines to analyze for the QC report" help= "Number of lines to consider for the qc test run." value='1000000' /> </inputs> <outputs> <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" /> </outputs> <tests> <test expect_num_outputs="2"> <repeat name="samFiles"> <param name="samFile" value="small_test_R1_unsorted.sam" /> </repeat> <repeat name="samFiles"> <param name="samFile" value="small_test_R2_unsorted.sam" /> </repeat> <param name='restrictionCutFile' value='DpnII_10k.bed' /> <param name='restrictionSequence' value='GATC' /> <param name='danglingSequence' value='GATC' /> <param name="lines" value='1000' /> <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2' /> </test> </tests> <help><![CDATA[ Quick QC ======== 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. 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. For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html ]]> </help> <expand macro="citations" /> </tool>