Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/CleanTranscriptFile.xml @ 36:44d5973c188c
Uploaded
| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 15:02:29 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 35:d94018ca4ada | 36:44d5973c188c |
|---|---|
| 1 <tool id="CleanTranscriptFile" name="clean Transcript File"> | |
| 2 <description>Clean a transcript file so that it is useable for S-MART.</description> | |
| 3 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName | |
| 4 #if $formatType.FormatInputFileName == 'gff': | |
| 5 -f gff | |
| 6 #elif $formatType.FormatInputFileName == 'gtf': | |
| 7 -f gtf | |
| 8 #elif $formatType.FormatInputFileName == 'gff3': | |
| 9 -f gff3 | |
| 10 #end if | |
| 11 #if $optionType.type == 'Yes': | |
| 12 -t $optionType.value | |
| 13 #end if | |
| 14 -o $outputFile | |
| 15 </command> | |
| 16 | |
| 17 <inputs> | |
| 18 <conditional name="formatType"> | |
| 19 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 20 <option value="gff">gff</option> | |
| 21 <option value="gtf">gtf</option> | |
| 22 <option value="gff3">gff3</option> | |
| 23 </param> | |
| 24 <when value="gff"> | |
| 25 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 26 </when> | |
| 27 <when value="gtf"> | |
| 28 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 29 </when> | |
| 30 <when value="gff3"> | |
| 31 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 32 </when> | |
| 33 </conditional> | |
| 34 | |
| 35 <conditional name="optionType"> | |
| 36 | |
| 37 <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)"> | |
| 38 <option value="Yes">Yes</option> | |
| 39 <option value="No" selected="true">No</option> | |
| 40 </param> | |
| 41 <when value="Yes"> | |
| 42 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/> | |
| 43 </when> | |
| 44 <when value="No"> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 | |
| 48 </inputs> | |
| 49 | |
| 50 | |
| 51 <outputs> | |
| 52 <data name="outputFile" format="gtf"> | |
| 53 <change_format> | |
| 54 <when input="formatType.FormatInputFileName" value="gff" format="gff" /> | |
| 55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" /> | |
| 56 </change_format> | |
| 57 </data> | |
| 58 | |
| 59 </outputs> | |
| 60 <tests> | |
| 61 <test> | |
| 62 <param name="FormatInputFileName" value="gtf" /> | |
| 63 <param name="inputFileName" value="genes.gtf" /> | |
| 64 <param name="type" value="No" /> | |
| 65 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" /> | |
| 66 </test> | |
| 67 </tests> | |
| 68 | |
| 69 <help> | |
| 70 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). | |
| 71 </help> | |
| 72 | |
| 73 </tool> |