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view pyCRAC/pyExtractLinesFromGTF.xml @ 1:7c9574213c0a draft default tip
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author | swebb |
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date | Thu, 20 Jun 2013 12:13:43 -0400 |
parents | 19b20927172d |
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<tool id ="pyExtractLinesFromGTF" name="pyExtractLinesFromGTF"> <requirements> <requirement type="package">pyCRAC</requirement> </requirements> <command interpreter="python"> /usr/local/bin/pyExtractLinesFromGTF.py --gtf $addGTF.gtf --genes_file $g --attribute $attribute $v -o $out </command> <version_command>/usr/local/bin/pyExtractLinesFromGTF.py --version</version_command> <inputs> <conditional name="addGTF"> <param name="gtfFile" type="select" label="Choose GTF File from"> <option value="default" selected="true">Defaults</option> <option value="other">History</option> </param> <when value="default"> <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"> <options from_data_table="pycrac_gtf"/> </param> </when> <when value="other"> <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/> </when> </conditional> <param format="txt" name="g" type="data" label="File containing gene list --genes_file" help="Tabular file with 1 column of gene or annotation names"/> <param name="attribute" type="select" label="Select the attribute to extract names from --attribute"> <option value="gene_name" selected="true">gene_name</option> <option value="gene_id">gene_id</option> <option value="transcript_name">transcript_name</option> <option value="transcript_id">transcript_id</option> </param> <param name="v" type="select" label="Extract lines from GTF that -v"> <option value="" selected="true">Match the gene file</option> <option value="-v">Do not match in gene fil</option> </param> <param name="label" type="text" format="txt" size="30" value="pyExtractLinesFromGTF" label="Enter output file label -o" /> </inputs> <outputs> <data format="gtf" name="out" label="${label.value}.gtf"/> </outputs> <help> .. class:: infomark **pyExtractLinesFromGTF** pyExtractLinesFromGTF is part of the pyCRAC_ package. Extracts lines from a GTF file that contain gene names of interest. .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html ------ **Parameter list** Options:: --gtf=Yourfavoritegtf.gtf type the path to the gtf file that you want to use. By default it expects data from the standard input. -g FILE, --genes_file=FILE name of your gene list or annotations list file (1 column) -o OUTFILE, --outfile=OUTFILE type the name and path of the file you want to write the output to. Default is standard output -a ATTRIBUTE, --attribute=ATTRIBUTE from which attribute do you want to extract names? Choices: gene_name, gene_id, transcript_name, transcript_id -v similar to grep -v option. Remove the genes from the GTF that are in the gene list </help> </tool>