Mercurial > repos > bgruening > hicexplorer_hicquickqc
diff 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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--- a/hicQuickQC.xml Fri Dec 11 21:05:59 2020 +0000 +++ b/hicQuickQC.xml Tue Mar 16 15:08:31 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<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> @@ -16,6 +16,8 @@ '${repeat.samFile}' #end for + --restrictionCutFile '$restrictionCutFile' + #if $restrictionSequence: --restrictionSequence '$restrictionSequence' #end if @@ -30,56 +32,43 @@ && mv ./QCfolder/* $qc.files_path/ && mv $qc.files_path/hicQC.html $qc && mv $qc.files_path/*.log raw_qc - ]]></command> + ]]> </command> <inputs> - <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"/> + <!-- 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> - - <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" - help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or - "dangling-ends". If not given, such statistics will not be available." /> + <expand macro="restrictionCutFile" /> + <expand macro="restrictionSequence" /> + <expand macro="danglingSequence" /> - <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence" - help="Sequence left by the restriction enzyme after cutting. - Each restriction enzyme recognizes a different DNA sequence and, - after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence. - For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. - For DpnII, the restriction site and dangling end sequence are the same: GATC. - This information is easily found on the description of the restriction enzyme. - The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. - A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/> - - <param argument="--lines" optional='true' type="integer" label="Lines" help= "Number of lines to consider for the qc test run." value='1000000'/> + <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 ${on_string}" /> + <data name="qc" format="html" label="${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> + <test expect_num_outputs="2"> <repeat name="samFiles"> - <param name="samFile" value="small_test_R1_unsorted.sam"/> + <param name="samFile" value="small_test_R1_unsorted.sam" /> </repeat> <repeat name="samFiles"> - <param name="samFile" value="small_test_R2_unsorted.sam"/> + <param name="samFile" value="small_test_R2_unsorted.sam" /> </repeat> - <conditional name="restrictionCutFileBinSize_conditional"> - <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/> - <repeat name='binSizes'> - <param name="binSize" value="5000"/> - </repeat> - </conditional> - <param name="lines" value='1000'/> - <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2'/> + <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. @@ -88,6 +77,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>