Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/SelectByTag.xml @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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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> |