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comparison SMART/galaxy/SelectByTag.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
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14:c79b9ae3f65f 15:440ceca58672
1 <tool id="SelectByTag" name="select by tag"> 1 <tool id="SelectByTag" name="select by tag">
2 <description>Keeps the genomic coordinates such that a value of a given tag.</description> 2 <description>Keep the genomic coordinates such that a value of a given tag.</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 ../Java/Python/SelectByTag.py -i $formatType.inputFileName 4 ../Java/Python/SelectByTag.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff': 5 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff 6 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2': 7 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2 8 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3': 9 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3 10 -f gff3
13 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName == 'gtf': 11 #elif $formatType.FormatInputFileName == 'gtf':
16 -f gtf 12 -f gtf
17 #end if 13 #end if
18 14
19 -g $Tag 15 -g $Tag
35 </command> 31 </command>
36 32
37 <inputs> 33 <inputs>
38 <conditional name="formatType"> 34 <conditional name="formatType">
39 <param name="FormatInputFileName" type="select" label="Input File Format"> 35 <param name="FormatInputFileName" type="select" label="Input File Format">
40 <option value="bed">bed</option>
41 <option value="gff">gff</option> 36 <option value="gff">gff</option>
42 <option value="gff2">gff2</option> 37 <option value="gff2">gff2</option>
43 <option value="gff3">gff3</option> 38 <option value="gff3">gff3</option>
44 <option value="sam">sam</option>
45 <option value="gtf">gtf</option> 39 <option value="gtf">gtf</option>
46 </param> 40 </param>
47 <when value="bed">
48 <param name="inputFileName" format="bed" type="data" label="Input File"/>
49 </when>
50 <when value="gff"> 41 <when value="gff">
51 <param name="inputFileName" format="gff" type="data" label="Input File"/> 42 <param name="inputFileName" format="gff" type="data" label="Input File"/>
52 </when> 43 </when>
53 <when value="gff2"> 44 <when value="gff2">
54 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 45 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
55 </when> 46 </when>
56 <when value="gff3"> 47 <when value="gff3">
57 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 48 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
58 </when> 49 </when>
59 <when value="sam">
60 <param name="inputFileName" format="sam" type="data" label="Input File"/>
61 </when>
62 <when value="gtf"> 50 <when value="gtf">
63 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 51 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
64 </when> 52 </when>
65 </conditional> 53 </conditional>
66 54
67 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> 55 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
68 56
69 <conditional name="OptionValue"> 57 <conditional name="OptionValue">
70 <param name="Value" type="select" label="value of tag"> 58 <param name="Value" type="select" label="given value for the tag">
71 <option value="Yes">Yes</option> 59 <option value="Yes">Yes</option>
72 <option value="No" selected="true">No</option> 60 <option value="No" selected="true">No</option>
73 </param> 61 </param>
74 <when value="Yes"> 62 <when value="Yes">
75 <param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> 63 <param name="valeur" type="integer" value="1"/>
76 </when> 64 </when>
77 <when value="No"> 65 <when value="No">
78 </when> 66 </when>
79 </conditional> 67 </conditional>
80 68
82 <param name="maximum" type="select" label="maximum value of tag"> 70 <param name="maximum" type="select" label="maximum value of tag">
83 <option value="Yes">Yes</option> 71 <option value="Yes">Yes</option>
84 <option value="No" selected="true">No</option> 72 <option value="No" selected="true">No</option>
85 </param> 73 </param>
86 <when value="Yes"> 74 <when value="Yes">
87 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> 75 <param name="max" type="integer" value="1"/>
88 </when> 76 </when>
89 <when value="No"> 77 <when value="No">
90 </when> 78 </when>
91 </conditional> 79 </conditional>
92 80
94 <param name="minimum" type="select" label="minimum value of tag"> 82 <param name="minimum" type="select" label="minimum value of tag">
95 <option value="Yes">Yes</option> 83 <option value="Yes">Yes</option>
96 <option value="No" selected="true">No</option> 84 <option value="No" selected="true">No</option>
97 </param> 85 </param>
98 <when value="Yes"> 86 <when value="Yes">
99 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> 87 <param name="min" type="integer" value="1"/>
100 </when> 88 </when>
101 <when value="No"> 89 <when value="No">
102 </when> 90 </when>
103 </conditional> 91 </conditional>
104 92
105 <conditional name="OptionDefault"> 93 <conditional name="OptionDefault">
106 <param name="default" type="select" label="gives this value if tag is not present"> 94 <param name="default" type="select" label="give this value if tag is not present">
107 <option value="Yes">Yes</option> 95 <option value="Yes">Yes</option>
108 <option value="No" selected="true">No</option> 96 <option value="No" selected="true">No</option>
109 </param> 97 </param>
110 <when value="Yes"> 98 <when value="Yes">
111 <param name="defaultValue" type="float" value="0" /> 99 <param name="defaultValue" type="float" value="0" />
117 105
118 <outputs> 106 <outputs>
119 <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/> 107 <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/>
120 </outputs> 108 </outputs>
121 109
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>
122 </tool> 119 </tool>