Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/SelectByTag.xml @ 15:440ceca58672
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author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:08:07 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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14:c79b9ae3f65f | 15:440ceca58672 |
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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> |