Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/CleanTranscriptFile.xml @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
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| children |
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| 37:d22fadc825e3 | 38:2c0c0a89fad7 |
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| 1 <tool id="CleanTranscriptFile" name="clean transcript file"> | |
| 2 <description>Clean a transcript file so that it is useable for S-MART.</description> | |
| 3 <requirements> | |
| 4 <requirement type="set_environment">PYTHONPATH</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName | |
| 7 #if $formatType.FormatInputFileName == 'gff': | |
| 8 -f gff | |
| 9 #elif $formatType.FormatInputFileName == 'gtf': | |
| 10 -f gtf | |
| 11 #elif $formatType.FormatInputFileName == 'gff3': | |
| 12 -f gff3 | |
| 13 #end if | |
| 14 #if $optionType.type == 'Yes': | |
| 15 -t $optionType.value | |
| 16 #end if | |
| 17 -o $outputFile | |
| 18 </command> | |
| 19 | |
| 20 <inputs> | |
| 21 <conditional name="formatType"> | |
| 22 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 23 <option value="gff">gff</option> | |
| 24 <option value="gtf">gtf</option> | |
| 25 <option value="gff3">gff3</option> | |
| 26 </param> | |
| 27 <when value="gff"> | |
| 28 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 29 </when> | |
| 30 <when value="gtf"> | |
| 31 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 32 </when> | |
| 33 <when value="gff3"> | |
| 34 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 | |
| 38 <conditional name="optionType"> | |
| 39 | |
| 40 <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)"> | |
| 41 <option value="Yes">Yes</option> | |
| 42 <option value="No" selected="true">No</option> | |
| 43 </param> | |
| 44 <when value="Yes"> | |
| 45 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/> | |
| 46 </when> | |
| 47 <when value="No"> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 | |
| 51 </inputs> | |
| 52 | |
| 53 | |
| 54 <outputs> | |
| 55 <data name="outputFile" format="gtf"> | |
| 56 <change_format> | |
| 57 <when input="formatType.FormatInputFileName" value="gtf" format="gtf" /> | |
| 58 <when input="formatType.FormatInputFileName" value="gff" format="gff" /> | |
| 59 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" /> | |
| 60 </change_format> | |
| 61 </data> | |
| 62 | |
| 63 </outputs> | |
| 64 <tests> | |
| 65 <test> | |
| 66 <param name="FormatInputFileName" value="gtf" /> | |
| 67 <param name="inputFileName" value="genes.gtf" /> | |
| 68 <param name="type" value="No" /> | |
| 69 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" /> | |
| 70 </test> | |
| 71 </tests> | |
| 72 | |
| 73 <help> | |
| 74 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). | |
| 75 </help> | |
| 76 | |
| 77 </tool> |