Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/CleanTranscriptFile.xml @ 27:4e7ee5683ef1
Deleted selected files
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:30:11 -0400 |
parents | 94ab73e8a190 |
children | 0ab839023fe4 |
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<tool id="CleanTranscriptFile" name="clean transcript file"> <description>Clean a transcript file so that it is useable for S-MART.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName #if $formatType.FormatInputFileName == 'gff': -f gff #elif $formatType.FormatInputFileName == 'gtf': -f gtf #elif $formatType.FormatInputFileName == 'gff3': -f gff3 #end if #if $optionType.type == 'Yes': -t $optionType.value #end if -o $outputFile </command> <inputs> <conditional name="formatType"> <param name="FormatInputFileName" type="select" label="Input File Format"> <option value="gff">gff</option> <option value="gtf">gtf</option> <option value="gff3">gff3</option> </param> <when value="gff"> <param name="inputFileName" format="gff" type="data" label="Input File"/> </when> <when value="gtf"> <param name="inputFileName" format="gtf" type="data" label="Input File"/> </when> <when value="gff3"> <param name="inputFileName" format="gff3" type="data" label="Input File"/> </when> </conditional> <conditional name="optionType"> <param name="type" type="select" label="You can choose the tag that you are interested in, like tRNA,rRNA,ncRNA,CDS,exon, etc." help="Name of the types you want to keep in GFF/GTF (list separated by commas)"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data name="outputFile" format="gtf"> <change_format> <when input="formatType.FormatInputFileName" value="gtf" format="gtf" /> <when input="formatType.FormatInputFileName" value="gff" format="gff" /> <when input="formatType.FormatInputFileName" value="gff3" format="gff3" /> </change_format> </data> </outputs> <tests> <test> <param name="FormatInputFileName" value="gtf" /> <param name="inputFileName" value="genes.gtf" /> <param name="type" value="No" /> <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" /> </test> </tests> <help> A GFF/GTF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about the GFF3 format, and http://mblab.wustl.edu/GTF22.html for the GTF format) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input file to keep the information you really want, based on the feature (3rd column). </help> </tool>