Mercurial > repos > sblanck > mpagenomics
view segmentFracB.xml @ 0:4d539083cf7f draft
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
| author | sblanck |
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| date | Tue, 12 May 2020 10:40:36 -0400 |
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<tool id="segFracB" name="Segmentation of allele B fraction " force_history_refresh="True" version="1.0.0"> <description></description> <command> <![CDATA[ Rscript ${__tool_directory__}/segmentFracB.R --chrom '$chrom' --input '$input' --output '$output' --new_file_path '$__new_file_path__' #if $settings.settingsType == "file": --settings_type '$settings.inputs' #end if #if $settings.settingsType == "dataset": --settings_type '$settings.settingsType' #end if --output_graph '$outputgraph' --zip_figures '$zipfigures' --settings_tumor '$tumorcsv' --outputlog '$outputlog' --log '$log' --userid '$__user_id__' --method '$method' ]]> </command> <inputs> <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/> <conditional name="settings"> <param name="settingsType" type="select" label="Files selection Mode" help="Select the whole cel files dataset or pick-up only few files from the dataset"> <option value="dataset">Select whole dataset</option> <option value="file">Select file individually</option> </param> <when value="dataset" /> <when value="file"> <param name="inputs" type="select" format="cel" multiple="true" label="Cel files"> <options from_dataset="input"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> </when> </conditional> <param name="tumorcsv" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/> <!--param name="chrom" type="text" value="All" label="Chromosomes" help="Chromosomes to segment. Use comma to choose multiple chromosomes: e.g. 1, 3, 8. Use 'All' for a segmentation on all chromosomes" /--> <param name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="leave blank for all chromosomes"> <option value="All">All</option> <option value="1">chr 1</option> <option value="2">chr 2</option> <option value="3">chr 3</option> <option value="4">chr 4</option> <option value="5">chr 5</option> <option value="6">chr 6</option> <option value="7">chr 7</option> <option value="8">chr 8</option> <option value="9">chr 9</option> <option value="10">chr 10</option> <option value="11">chr 11</option> <option value="12">chr 12</option> <option value="13">chr 13</option> <option value="14">chr 14</option> <option value="15">chr 15</option> <option value="16">chr 16</option> <option value="17">chr 17</option> <option value="18">chr 18</option> <option value="19">chr 19</option> <option value="20">chr 20</option> <option value="21">chr 21</option> <option value="22">chr 22</option> <option value="23">chr 23</option> <option value="24">chr 24</option> <option value="25">chr 25</option> </param> <param name="method" type="select" label="Segmentation method" help=""> <option value="cghseg">cghseg</option> <option value="PELT">PELT</option> </param> <param name="outputgraph" type="select" label="Output figures"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> </param> <param name="outputlog" type="select" label="Output log"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> </param> </inputs> <outputs> <data format="sar" name="output" label="allele B fraction segmentation of ${input.name}" /> <data format="zip" name="zipfigures" label="allele B fraction segmentation figures of ${input.name}"> <filter>outputgraph == "TRUE"</filter> </data> <data format="log" name="log" label="log of allele B fraction segmentation of ${input.name}"> <filter>outputlog == "TRUE"</filter> </data> </outputs> <stdio> <exit_code range="1:" level="fatal" description="See logs for more details" /> </stdio> <help> .. class:: warningmark Data normalization must be run (with the data normalization tool) prior to segmentation. ----- **What it does** This tool segments allele B fraction extracted from the previously normalized data. This tools works only on normal-tumor study. Outputs: *A tabular text file containing 6 columns which describe all the segment (1 line per segment):* - sampleNames: Name of the file. - chrom: The chromosome of the segment. - chromStart: The starting position (in bp) of the segment. This position is not included in the segment. - chromEnd: The 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. *A .zip file containing all the figures (optionnal)* ----- **Normal-tumor csv files** Normal-tumor csv file is required to segment Allele B fraction, because naive genotyping is based on normal samples : - The first column contains the names of the files corresponding to normal samples of the dataset. - The second column contains the names of the tumor samples files. - Column names of these two columns are respectively normal and tumor. - Columns are separated by a comma. - *Extensions of the files (.CEL for example) should be removed* **Example** Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) :: patient1_normal.cel patient1_tumor.cel patient2_normal.cel patient2_tumor.cel patient3_normal.cel patient3_tumor.cel The csv file should look like this :: normal,tumor patient1_normal,patient1_tumor patient2_normal,patient2_tumor patient3_normal,patient3_tumor ----- **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>`_ If segmentation is performed with PELT, please cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. <http://arxiv.org/abs/1101.1438>`_ If segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. <http://www.ncbi.nlm.nih.gov/pubmed/15705208>`_ , and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. <http://arxiv.org/abs/1004.0887>`_ </help> </tool>