Mercurial > repos > sblanck > mpagenomics
view filter.xml @ 4:3fcbb8030fcc draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author | sblanck |
---|---|
date | Mon, 12 Apr 2021 14:47:09 +0000 |
parents | 4d539083cf7f |
children | 4f753bb8681e |
line wrap: on
line source
<tool id="callfilter" name="Filter" description="segmented and called data" version="1.2.0"> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> </requirements> <command> <![CDATA[ Rscript ${__tool_directory__}/filter.R --input '$input' --length '$length' --probes '$probes' --new_file_path '$output.extra_files_path' #if $settingsSNP.signal == "fracB": --nbcall 'normal' #else --nbcall '${settingsSNP.nbcall}' #end if --settings_signal '$settingsSNP.signal' --output '$output' --outputlog '$outputlog' --log '$log' ]]> </command> <inputs> <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/> <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/> <param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/> <conditional name="settingsSNP"> <param name="signal" type="select" multiple="false" label="Signal you want to work on"> <option value="CN">CN</option> <option value="fracB">fracB</option> </param> <when value="CN"> <param name="nbcall" type="select" multiple="true" label="Label(s) to keep"> <option value="double_loss">double loss</option> <option value="loss">loss</option> <option value="normal">normal</option> <option value="gain">gain</option> <option value="amplification">amplification</option> </param> </when> </conditional> <param name="outputlog" type="select" label="Output log"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> </param> </inputs> <outputs> <data format="tabular" name="output" label="filter of ${on_string}" /> <data format="log" name="log" label="log of filter of ${input.name}"> <filter>outputlog == "TRUE"</filter> </data> </outputs> <stdio> <exit_code range="1:" level="fatal" description="See logs for more details" /> </stdio> <help> **What it does** This tool filters results obtained by the segmentation and calling tool. ----- Input/Output file: *A tabular text file containing 7 columns:* - sampleNames: Name of the file. - chrom: Chromosome of the segment. - chromStart: Starting position (in bp) of the segment. This position is not included in the segment. - chromEnd: Ending position (in bp) of the segment. This position is included in the segment. - probes: Number of probes in the segment. - means: Mean of the segment. - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”). ----- **Citation** If you use this tool please cite : `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ </help> </tool>