comparison SMART/galaxy/restrictFromSize.xml @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 440ceca58672
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5:ea3082881bf8 6:769e306b7933
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 == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName == 'gtf':
16 -f gtf
17 #end if
18
19 #if $OptionMax.maximum == "Yes":
20 -M $OptionMax.max
21 #end if
22 #if $OptionMin.minimum == "Yes":
23 -m $OptionMin.min
24 #end if
25
26 -o $outputFileGff
27 </command>
28
29 <inputs>
30 <conditional name="formatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format">
32 <option value="bed">bed</option>
33 <option value="gff">gff</option>
34 <option value="gff2">gff2</option>
35 <option value="gff3">gff3</option>
36 <option value="sam">sam</option>
37 <option value="gtf">gtf</option>
38 </param>
39 <when value="bed">
40 <param name="inputFileName" format="bed" type="data" label="Input File"/>
41 </when>
42 <when value="gff">
43 <param name="inputFileName" format="gff" type="data" label="Input File"/>
44 </when>
45 <when value="gff2">
46 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
47 </when>
48 <when value="gff3">
49 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
50 </when>
51 <when value="sam">
52 <param name="inputFileName" format="sam" type="data" label="Input File"/>
53 </when>
54 <when value="gtf">
55 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
56 </when>
57 </conditional>
58
59 <conditional name="OptionMax">
60 <param name="maximum" type="select" label="maximum number of np">
61 <option value="Yes">Yes</option>
62 <option value="No" selected="true">No</option>
63 </param>
64 <when value="Yes">
65 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
66 </when>
67 <when value="No">
68 </when>
69 </conditional>
70
71 <conditional name="OptionMin">
72 <param name="minimum" type="select" label="minimum number of np">
73 <option value="Yes">Yes</option>
74 <option value="No" selected="true">No</option>
75 </param>
76 <when value="Yes">
77 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
78 </when>
79 <when value="No">
80 </when>
81 </conditional>
82
83 </inputs>
84
85 <outputs>
86 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/>
87 </outputs>
88
89 <help>
90 command example: restrictFromSize.py -i cis_e10_cluster20InSeed2515_nbEUp10.gff3 -f gff -o cis_e10_cluster20InSeed2515_nbEUp10_lgUp50 -m 50
91 </help>
92
93 </tool>