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comparison SMART/galaxy/SelectByTag.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 <tool id="SelectByTag" name="select by tag">
2 <description>Keep 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 #elif $formatType.FormatInputFileName == 'gff':
6 -f gff
7 #elif $formatType.FormatInputFileName == 'gff2':
8 -f gff2
9 #elif $formatType.FormatInputFileName == 'gff3':
10 -f gff3
11 #elif $formatType.FormatInputFileName == 'gtf':
12 -f gtf
13 #end if
14
15 -g $Tag
16 #if $OptionValue.Value == "Yes":
17 -a $OptionValue.valeur
18 #end if
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 #if $OptionDefault.default == "Yes":
27 -d $OptionDefault.defaultValue
28 #end if
29
30 -o $outputFileGff
31 </command>
32
33 <inputs>
34 <conditional name="formatType">
35 <param name="FormatInputFileName" type="select" label="Input File Format">
36 <option value="gff">gff</option>
37 <option value="gff2">gff2</option>
38 <option value="gff3">gff3</option>
39 <option value="gtf">gtf</option>
40 </param>
41 <when value="gff">
42 <param name="inputFileName" format="gff" type="data" label="Input File"/>
43 </when>
44 <when value="gff2">
45 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
46 </when>
47 <when value="gff3">
48 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
49 </when>
50 <when value="gtf">
51 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
52 </when>
53 </conditional>
54
55 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
56
57 <conditional name="OptionValue">
58 <param name="Value" type="select" label="given value for the tag">
59 <option value="Yes">Yes</option>
60 <option value="No" selected="true">No</option>
61 </param>
62 <when value="Yes">
63 <param name="valeur" type="integer" value="1"/>
64 </when>
65 <when value="No">
66 </when>
67 </conditional>
68
69 <conditional name="OptionMax">
70 <param name="maximum" type="select" label="maximum 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="max" type="integer" value="1"/>
76 </when>
77 <when value="No">
78 </when>
79 </conditional>
80
81 <conditional name="OptionMin">
82 <param name="minimum" type="select" label="minimum 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="min" type="integer" value="1"/>
88 </when>
89 <when value="No">
90 </when>
91 </conditional>
92
93 <conditional name="OptionDefault">
94 <param name="default" type="select" label="give this value if tag is not present">
95 <option value="Yes">Yes</option>
96 <option value="No" selected="true">No</option>
97 </param>
98 <when value="Yes">
99 <param name="defaultValue" type="float" value="0" />
100 </when>
101 <when value="No">
102 </when>
103 </conditional>
104 </inputs>
105
106 <outputs>
107 <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/>
108 </outputs>
109
110 <help>
111 The script reads a list of genomic coordinates and output all the features with specific tag values. If you want to know more about tags, please consult the GFF format page: http://www.sequenceontology.org/gff3.shtml
112
113 The tools reads the input file, and more specifically the tag that you specified. You can mention a lower and a upper bound for its value, or a specific value, and the tool will print all the features such that the tags are between the specified bounds or matches the string.
114
115 A tag has to be present for each feature. If not, you can specify a default value which will be used if the tag is absent.
116
117 This tool can be used to select the clusters with a minimum number of elements (the tag **nbElements** counts the number of elements per clusters) or to select the reads which have mapped less than *n* times (the tag **nbOccurrences** counts the number of mappings per read).
118 </help>
119 </tool>