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comparison SMART/galaxy/restrictFromSize.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
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14:c79b9ae3f65f 15:440ceca58672
1 <tool id="restrictFromSize" name="restrict from size"> 1 <tool id="restrictFromSize" name="restrict from size">
2 <description>Select the elements of a list of sequences or transcripts with a given size.</description> 2 <description>Select the elements of a list of sequences or transcripts with a given size.</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName 4 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'fasta':
6 -f fasta
7 #elif $formatType.FormatInputFileName == 'bed':
6 -f bed 8 -f bed
7 #elif $formatType.FormatInputFileName == 'gff': 9 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff 10 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2': 11 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2 12 -f gff2
27 </command> 29 </command>
28 30
29 <inputs> 31 <inputs>
30 <conditional name="formatType"> 32 <conditional name="formatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format"> 33 <param name="FormatInputFileName" type="select" label="Input File Format">
34 <option value="fasta">fasta</option>
32 <option value="bed">bed</option> 35 <option value="bed">bed</option>
33 <option value="gff">gff</option> 36 <option value="gff">gff</option>
34 <option value="gff2">gff2</option> 37 <option value="gff2">gff2</option>
35 <option value="gff3">gff3</option> 38 <option value="gff3">gff3</option>
36 <option value="sam">sam</option> 39 <option value="sam">sam</option>
37 <option value="gtf">gtf</option> 40 <option value="gtf">gtf</option>
38 </param> 41 </param>
42 <when value="fasta">
43 <param name="inputFileName" format="fasta" type="data" label="Input File"/>
44 </when>
39 <when value="bed"> 45 <when value="bed">
40 <param name="inputFileName" format="bed" type="data" label="Input File"/> 46 <param name="inputFileName" format="bed" type="data" label="Input File"/>
41 </when> 47 </when>
42 <when value="gff"> 48 <when value="gff">
43 <param name="inputFileName" format="gff" type="data" label="Input File"/> 49 <param name="inputFileName" format="gff" type="data" label="Input File"/>
85 <outputs> 91 <outputs>
86 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/> 92 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/>
87 </outputs> 93 </outputs>
88 94
89 <help> 95 <help>
90 command example: restrictFromSize.py -i cis_e10_cluster20InSeed2515_nbEUp10.gff3 -f gff -o cis_e10_cluster20InSeed2515_nbEUp10_lgUp50 -m 50 96 Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide.
91 </help> 97 </help>
92 98
93 </tool> 99 </tool>