Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/SelectByTag.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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1 <tool id="SelectByTag" name="select by tag"> | |
2 <description>Keeps the genomic coordinates such that a value of a given tag.</description> | |
3 <command interpreter="python"> | |
4 ../Java/Python/SelectByTag.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 -g $Tag | |
20 #if $OptionValue.Value == "Yes": | |
21 -a $OptionValue.valeur | |
22 #end if | |
23 #if $OptionMax.maximum == "Yes": | |
24 -M $OptionMax.max | |
25 #end if | |
26 #if $OptionMin.minimum == "Yes": | |
27 -m $OptionMin.min | |
28 #end if | |
29 | |
30 #if $OptionDefault.default == "Yes": | |
31 -d $OptionDefault.defaultValue | |
32 #end if | |
33 | |
34 -o $outputFileGff | |
35 </command> | |
36 | |
37 <inputs> | |
38 <conditional name="formatType"> | |
39 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
40 <option value="bed">bed</option> | |
41 <option value="gff">gff</option> | |
42 <option value="gff2">gff2</option> | |
43 <option value="gff3">gff3</option> | |
44 <option value="sam">sam</option> | |
45 <option value="gtf">gtf</option> | |
46 </param> | |
47 <when value="bed"> | |
48 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
49 </when> | |
50 <when value="gff"> | |
51 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
52 </when> | |
53 <when value="gff2"> | |
54 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
55 </when> | |
56 <when value="gff3"> | |
57 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
58 </when> | |
59 <when value="sam"> | |
60 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
61 </when> | |
62 <when value="gtf"> | |
63 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
64 </when> | |
65 </conditional> | |
66 | |
67 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> | |
68 | |
69 <conditional name="OptionValue"> | |
70 <param name="Value" type="select" label="value of tag"> | |
71 <option value="Yes">Yes</option> | |
72 <option value="No" selected="true">No</option> | |
73 </param> | |
74 <when value="Yes"> | |
75 <param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
76 </when> | |
77 <when value="No"> | |
78 </when> | |
79 </conditional> | |
80 | |
81 <conditional name="OptionMax"> | |
82 <param name="maximum" type="select" label="maximum value of tag"> | |
83 <option value="Yes">Yes</option> | |
84 <option value="No" selected="true">No</option> | |
85 </param> | |
86 <when value="Yes"> | |
87 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
88 </when> | |
89 <when value="No"> | |
90 </when> | |
91 </conditional> | |
92 | |
93 <conditional name="OptionMin"> | |
94 <param name="minimum" type="select" label="minimum value of tag"> | |
95 <option value="Yes">Yes</option> | |
96 <option value="No" selected="true">No</option> | |
97 </param> | |
98 <when value="Yes"> | |
99 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
100 </when> | |
101 <when value="No"> | |
102 </when> | |
103 </conditional> | |
104 | |
105 <conditional name="OptionDefault"> | |
106 <param name="default" type="select" label="gives this value if tag is not present"> | |
107 <option value="Yes">Yes</option> | |
108 <option value="No" selected="true">No</option> | |
109 </param> | |
110 <when value="Yes"> | |
111 <param name="defaultValue" type="float" value="0" /> | |
112 </when> | |
113 <when value="No"> | |
114 </when> | |
115 </conditional> | |
116 </inputs> | |
117 | |
118 <outputs> | |
119 <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/> | |
120 </outputs> | |
121 | |
122 </tool> |