Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/restrictFromSize.xml @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
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35:d94018ca4ada | 36:44d5973c188c |
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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 <command interpreter="python"> | |
4 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName | |
5 #if $formatType.FormatInputFileName == 'fasta': | |
6 -f fasta | |
7 #elif $formatType.FormatInputFileName == 'bed': | |
8 -f bed | |
9 #elif $formatType.FormatInputFileName == 'gff': | |
10 -f gff | |
11 #elif $formatType.FormatInputFileName == 'gff2': | |
12 -f gff2 | |
13 #elif $formatType.FormatInputFileName == 'gff3': | |
14 -f gff3 | |
15 #elif $formatType.FormatInputFileName == 'sam': | |
16 -f sam | |
17 #elif $formatType.FormatInputFileName == 'gtf': | |
18 -f gtf | |
19 #end if | |
20 | |
21 #if $OptionMax.maximum == "Yes": | |
22 -M $OptionMax.max | |
23 #end if | |
24 #if $OptionMin.minimum == "Yes": | |
25 -m $OptionMin.min | |
26 #end if | |
27 | |
28 -o $outputFileGff | |
29 </command> | |
30 | |
31 <inputs> | |
32 <conditional name="formatType"> | |
33 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
34 <option value="fasta">fasta</option> | |
35 <option value="bed">bed</option> | |
36 <option value="gff">gff</option> | |
37 <option value="gff2">gff2</option> | |
38 <option value="gff3">gff3</option> | |
39 <option value="sam">sam</option> | |
40 <option value="gtf">gtf</option> | |
41 </param> | |
42 <when value="fasta"> | |
43 <param name="inputFileName" format="fasta" type="data" label="Input File"/> | |
44 </when> | |
45 <when value="bed"> | |
46 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
47 </when> | |
48 <when value="gff"> | |
49 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
50 </when> | |
51 <when value="gff2"> | |
52 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
53 </when> | |
54 <when value="gff3"> | |
55 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
56 </when> | |
57 <when value="sam"> | |
58 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
59 </when> | |
60 <when value="gtf"> | |
61 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
62 </when> | |
63 </conditional> | |
64 | |
65 <conditional name="OptionMax"> | |
66 <param name="maximum" type="select" label="maximum number of np"> | |
67 <option value="Yes">Yes</option> | |
68 <option value="No" selected="true">No</option> | |
69 </param> | |
70 <when value="Yes"> | |
71 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
72 </when> | |
73 <when value="No"> | |
74 </when> | |
75 </conditional> | |
76 | |
77 <conditional name="OptionMin"> | |
78 <param name="minimum" type="select" label="minimum number of np"> | |
79 <option value="Yes">Yes</option> | |
80 <option value="No" selected="true">No</option> | |
81 </param> | |
82 <when value="Yes"> | |
83 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
84 </when> | |
85 <when value="No"> | |
86 </when> | |
87 </conditional> | |
88 | |
89 </inputs> | |
90 | |
91 <outputs> | |
92 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/> | |
93 </outputs> | |
94 | |
95 <help> | |
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. | |
97 </help> | |
98 | |
99 </tool> |