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comparison SMART/galaxy/restrictFromSize.xml @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
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 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName 4 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'fasta': 5 #if $formatType.FormatInputFileName == 'bed':
9 -f fasta
10 #elif $formatType.FormatInputFileName == 'bed':
11 -f bed 6 -f bed
12 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
13 -f gff 8 -f gff
14 #elif $formatType.FormatInputFileName == 'gff2': 9 #elif $formatType.FormatInputFileName == 'gff2':
15 -f gff2 10 -f gff2
32 </command> 27 </command>
33 28
34 <inputs> 29 <inputs>
35 <conditional name="formatType"> 30 <conditional name="formatType">
36 <param name="FormatInputFileName" type="select" label="Input File Format"> 31 <param name="FormatInputFileName" type="select" label="Input File Format">
37 <option value="fasta">fasta</option>
38 <option value="bed">bed</option> 32 <option value="bed">bed</option>
39 <option value="gff">gff</option> 33 <option value="gff">gff</option>
40 <option value="gff2">gff2</option> 34 <option value="gff2">gff2</option>
41 <option value="gff3">gff3</option> 35 <option value="gff3">gff3</option>
42 <option value="sam">sam</option> 36 <option value="sam">sam</option>
43 <option value="gtf">gtf</option> 37 <option value="gtf">gtf</option>
44 </param> 38 </param>
45 <when value="fasta">
46 <param name="inputFileName" format="fasta" type="data" label="Input File"/>
47 </when>
48 <when value="bed"> 39 <when value="bed">
49 <param name="inputFileName" format="bed" type="data" label="Input File"/> 40 <param name="inputFileName" format="bed" type="data" label="Input File"/>
50 </when> 41 </when>
51 <when value="gff"> 42 <when value="gff">
52 <param name="inputFileName" format="gff" type="data" label="Input File"/> 43 <param name="inputFileName" format="gff" type="data" label="Input File"/>
90 </conditional> 81 </conditional>
91 82
92 </inputs> 83 </inputs>
93 84
94 <outputs> 85 <outputs>
95 <data name="outputFileGff" format="gff3" label="[restrict from size] output file"/> 86 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/>
96 </outputs> 87 </outputs>
97 88
98 <help> 89 <help>
99 Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide. 90 command example: restrictFromSize.py -i cis_e10_cluster20InSeed2515_nbEUp10.gff3 -f gff -o cis_e10_cluster20InSeed2515_nbEUp10_lgUp50 -m 50
100 </help> 91 </help>
101 92
102 </tool> 93 </tool>