Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/restrictFromSize.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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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> | |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName | |
8 #if $formatType.FormatInputFileName == 'fasta': | |
9 -f fasta | |
10 #elif $formatType.FormatInputFileName == 'bed': | |
11 -f bed | |
12 #elif $formatType.FormatInputFileName == 'gff': | |
13 -f gff | |
14 #elif $formatType.FormatInputFileName == 'gff2': | |
15 -f gff2 | |
16 #elif $formatType.FormatInputFileName == 'gff3': | |
17 -f gff3 | |
18 #elif $formatType.FormatInputFileName == 'sam': | |
19 -f sam | |
20 #elif $formatType.FormatInputFileName == 'gtf': | |
21 -f gtf | |
22 #end if | |
23 | |
24 #if $OptionMax.maximum == "Yes": | |
25 -M $OptionMax.max | |
26 #end if | |
27 #if $OptionMin.minimum == "Yes": | |
28 -m $OptionMin.min | |
29 #end if | |
30 | |
31 -o $outputFileGff | |
32 </command> | |
33 | |
34 <inputs> | |
35 <conditional name="formatType"> | |
36 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
37 <option value="fasta">fasta</option> | |
38 <option value="bed">bed</option> | |
39 <option value="gff">gff</option> | |
40 <option value="gff2">gff2</option> | |
41 <option value="gff3">gff3</option> | |
42 <option value="sam">sam</option> | |
43 <option value="gtf">gtf</option> | |
44 </param> | |
45 <when value="fasta"> | |
46 <param name="inputFileName" format="fasta" type="data" label="Input File"/> | |
47 </when> | |
48 <when value="bed"> | |
49 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
50 </when> | |
51 <when value="gff"> | |
52 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
53 </when> | |
54 <when value="gff2"> | |
55 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
56 </when> | |
57 <when value="gff3"> | |
58 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
59 </when> | |
60 <when value="sam"> | |
61 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
62 </when> | |
63 <when value="gtf"> | |
64 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
65 </when> | |
66 </conditional> | |
67 | |
68 <conditional name="OptionMax"> | |
69 <param name="maximum" type="select" label="maximum number of np"> | |
70 <option value="Yes">Yes</option> | |
71 <option value="No" selected="true">No</option> | |
72 </param> | |
73 <when value="Yes"> | |
74 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
75 </when> | |
76 <when value="No"> | |
77 </when> | |
78 </conditional> | |
79 | |
80 <conditional name="OptionMin"> | |
81 <param name="minimum" type="select" label="minimum number of np"> | |
82 <option value="Yes">Yes</option> | |
83 <option value="No" selected="true">No</option> | |
84 </param> | |
85 <when value="Yes"> | |
86 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
87 </when> | |
88 <when value="No"> | |
89 </when> | |
90 </conditional> | |
91 | |
92 </inputs> | |
93 | |
94 <outputs> | |
95 <data name="outputFileGff" format="gff3" label="[restrict from size] output file"/> | |
96 </outputs> | |
97 | |
98 <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. | |
100 </help> | |
101 | |
102 </tool> |