|
36
|
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>
|
