Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
parents
children 440ceca58672
comparison
equal deleted inserted replaced
5:ea3082881bf8 6:769e306b7933
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>