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comparison SMART/galaxy/SelectByTag.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
1 <tool id="SelectByTag" name="select by tag"> 1 <tool id="SelectByTag" name="select by tag">
2 <description>Keep the genomic coordinates such that a value of a given tag.</description> 2 <description>Keeps the genomic coordinates such that a value of a given tag.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/SelectByTag.py -i $formatType.inputFileName 4 ../Java/Python/SelectByTag.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
8 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
9 -f gff 8 -f gff
10 #elif $formatType.FormatInputFileName == 'gff2': 9 #elif $formatType.FormatInputFileName == 'gff2':
11 -f gff2 10 -f gff2
12 #elif $formatType.FormatInputFileName == 'gff3': 11 #elif $formatType.FormatInputFileName == 'gff3':
13 -f gff3 12 -f gff3
13 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
14 #elif $formatType.FormatInputFileName == 'gtf': 15 #elif $formatType.FormatInputFileName == 'gtf':
15 -f gtf 16 -f gtf
16 #end if 17 #end if
17 18
18 -g $Tag 19 -g $Tag
34 </command> 35 </command>
35 36
36 <inputs> 37 <inputs>
37 <conditional name="formatType"> 38 <conditional name="formatType">
38 <param name="FormatInputFileName" type="select" label="Input File Format"> 39 <param name="FormatInputFileName" type="select" label="Input File Format">
40 <option value="bed">bed</option>
39 <option value="gff">gff</option> 41 <option value="gff">gff</option>
40 <option value="gff2">gff2</option> 42 <option value="gff2">gff2</option>
41 <option value="gff3">gff3</option> 43 <option value="gff3">gff3</option>
44 <option value="sam">sam</option>
42 <option value="gtf">gtf</option> 45 <option value="gtf">gtf</option>
43 </param> 46 </param>
47 <when value="bed">
48 <param name="inputFileName" format="bed" type="data" label="Input File"/>
49 </when>
44 <when value="gff"> 50 <when value="gff">
45 <param name="inputFileName" format="gff" type="data" label="Input File"/> 51 <param name="inputFileName" format="gff" type="data" label="Input File"/>
46 </when> 52 </when>
47 <when value="gff2"> 53 <when value="gff2">
48 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 54 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
49 </when> 55 </when>
50 <when value="gff3"> 56 <when value="gff3">
51 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 57 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
52 </when> 58 </when>
59 <when value="sam">
60 <param name="inputFileName" format="sam" type="data" label="Input File"/>
61 </when>
53 <when value="gtf"> 62 <when value="gtf">
54 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 63 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
55 </when> 64 </when>
56 </conditional> 65 </conditional>
57 66
58 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> 67 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
59 68
60 <conditional name="OptionValue"> 69 <conditional name="OptionValue">
61 <param name="Value" type="select" label="given value for the tag"> 70 <param name="Value" type="select" label="value of tag">
62 <option value="Yes">Yes</option> 71 <option value="Yes">Yes</option>
63 <option value="No" selected="true">No</option> 72 <option value="No" selected="true">No</option>
64 </param> 73 </param>
65 <when value="Yes"> 74 <when value="Yes">
66 <param name="valeur" type="integer" value="1"/> 75 <param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
67 </when> 76 </when>
68 <when value="No"> 77 <when value="No">
69 </when> 78 </when>
70 </conditional> 79 </conditional>
71 80
73 <param name="maximum" type="select" label="maximum value of tag"> 82 <param name="maximum" type="select" label="maximum value of tag">
74 <option value="Yes">Yes</option> 83 <option value="Yes">Yes</option>
75 <option value="No" selected="true">No</option> 84 <option value="No" selected="true">No</option>
76 </param> 85 </param>
77 <when value="Yes"> 86 <when value="Yes">
78 <param name="max" type="integer" value="1"/> 87 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
79 </when> 88 </when>
80 <when value="No"> 89 <when value="No">
81 </when> 90 </when>
82 </conditional> 91 </conditional>
83 92
85 <param name="minimum" type="select" label="minimum value of tag"> 94 <param name="minimum" type="select" label="minimum value of tag">
86 <option value="Yes">Yes</option> 95 <option value="Yes">Yes</option>
87 <option value="No" selected="true">No</option> 96 <option value="No" selected="true">No</option>
88 </param> 97 </param>
89 <when value="Yes"> 98 <when value="Yes">
90 <param name="min" type="integer" value="1"/> 99 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
91 </when> 100 </when>
92 <when value="No"> 101 <when value="No">
93 </when> 102 </when>
94 </conditional> 103 </conditional>
95 104
96 <conditional name="OptionDefault"> 105 <conditional name="OptionDefault">
97 <param name="default" type="select" label="give this value if tag is not present"> 106 <param name="default" type="select" label="gives this value if tag is not present">
98 <option value="Yes">Yes</option> 107 <option value="Yes">Yes</option>
99 <option value="No" selected="true">No</option> 108 <option value="No" selected="true">No</option>
100 </param> 109 </param>
101 <when value="Yes"> 110 <when value="Yes">
102 <param name="defaultValue" type="float" value="0" /> 111 <param name="defaultValue" type="float" value="0" />
105 </when> 114 </when>
106 </conditional> 115 </conditional>
107 </inputs> 116 </inputs>
108 117
109 <outputs> 118 <outputs>
110 <data name="outputFileGff" format="gff3" label="[select by tag] output file"/> 119 <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/>
111 </outputs> 120 </outputs>
112 121
113 <help>
114 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
115
116 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.
117
118 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.
119
120 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).
121 </help>
122 </tool> 122 </tool>