Mercurial > repos > sblanck > mpagenomics
view extractCN.xml @ 6:7076911e5c64 draft default tip
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit a644ed69951bcc1ac46426c5e6c9a0af1003a9a8-dirty"
| author | sblanck |
|---|---|
| date | Tue, 20 Apr 2021 15:00:42 +0000 |
| parents | 4f753bb8681e |
| children |
line wrap: on
line source
<tool id="extract" name="Extract" version="1.3.0"> <description>copy number or allele B fraction signal</description> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> </requirements> <command> <![CDATA[ Rscript ${__tool_directory__}/extractCN.R --chrom '$chrom' --input '$input' --zip '$zip' #if $settings.settingsType == "file": --settings_type '$settings.inputs' #end if #if $settings.settingsType == "dataset": --settings_type 'dataset' #end if #if $settingsSNP.signal == "fracB": --new_file_path '$outputF.extra_files_path' --output '$outputF' --settings_snp 'TRUE' --settings_tumor '$settingsSNP.tumorcsvFracBsym' --symmetrize 'TRUE' #else --new_file_path '$outputC.extra_files_path' --output '$outputC' --settings_snp '$settingsSNP.snp' #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard": --settings_tumor 'None' #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor": --settings_tumor '${settingsSNP.settingsTumor.tumorcsvCN}' #end if #end if --outputlog '$outputlog' --log '$log' --settings_signal '$settingsSNP.signal' --userid '$__user_id__' ]]> </command> <inputs> <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/> <param name="zip" type="data" format="nzip" label="Zip results file" help="Zip results 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> <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="fracB"> <!--conditional name="sym"> <param name="symmetrize" type="select" label="Symmetrize allele B signal"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> </param> <when value="TRUE"--> <param name="tumorcsvFracBsym" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/> <!--/when> <when value="FALSE"> <conditional name="settingsTumorFracB"> <param name="settingsTypeTumorFracB" type="select" label="Reference"> <option value="standard">Study without reference</option> <option value="tumor">Normal-tumor study</option> </param> <when value="standard"/> <when value="tumor"> <param name="tumorcsvFracB" type="data" format="csv" label="Tumor boost csv file" help="Normal-tumor csv file. See below for more information."/> </when> </conditional> </when--> <!--/conditional--> </when> <when value="CN"> <conditional name="settingsTumor"> <param name="settingsTypeTumor" type="select" label="Reference"> <option value="standard">Study without reference</option> <option value="tumor">Normal-tumor study</option> </param> <when value="standard"/> <when value="tumor"> <param name="tumorcsvCN" type="data" format="csv" label="Normal tumor csv file" help="Normal-tumor csv file. See below for more information."/> </when> </conditional> <param name="snp" type="select" label="Select Probes"> <option value="FALSE">CN and SNP probes</option> <option value="TRUE">Only SNP probes</option> </param> </when> </conditional> <!--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="You can select several chromosomeleave blank for all chromosomes"> <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="outputlog" type="select" label="Output log"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> </param> </inputs> <outputs> <data format="saf" name="outputF" label="signal extraction of ${settingsSNP.signal} of ${input.name}"> <filter>settingsSNP['signal']=='fracB'</filter> </data> <data format="sef" name="outputC" label="signal extraction of ${settingsSNP.signal} of ${input.name}"> <filter>settingsSNP['signal']=='CN'</filter> </data> <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} 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 signal extraction. ----- **What it does** This tool extracts the copy number profile from the normalized data. Outputs: *A tabular text file containing 3 fixed columns and 1 column per sample:* - chr: Chromosome. - position: Genomic position (in bp). - probeNames: Name of the probes of the microarray. - One column per sample which contains the copy number profile for each sample. ----- **Normal-tumor study** In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided : - 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>`_ </help> </tool>