Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/modifyGenomicCoordinates.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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1 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates"> | |
2 <description>Extend or shrink a list of genomic coordinates.</description> | |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName | |
7 #if $formatType.FormatInputFileName == 'bed': | |
8 -f bed | |
9 #elif $formatType.FormatInputFileName == 'gff': | |
10 -f gff | |
11 #elif $formatType.FormatInputFileName == 'gff2': | |
12 -f gff2 | |
13 #elif $formatType.FormatInputFileName == 'gff3': | |
14 -f gff3 | |
15 #elif $formatType.FormatInputFileName == 'sam': | |
16 -f sam | |
17 #elif $formatType.FormatInputFileName == 'gtf': | |
18 -f gtf | |
19 #end if | |
20 | |
21 #if $OptionStart.start == "Yes": | |
22 -s $OptionStart.startValue | |
23 #end if | |
24 | |
25 #if $OptionEnd.end == "Yes": | |
26 -e $OptionEnd.endValue | |
27 #end if | |
28 | |
29 #if $OptionFivePrim.five == "Yes": | |
30 -5 $OptionFivePrim.fivePValue | |
31 #end if | |
32 | |
33 #if $OptionTroisP.TroisP == "Yes": | |
34 -3 $OptionTroisP.ThreePValue | |
35 #end if | |
36 | |
37 -o $outputFile | |
38 </command> | |
39 | |
40 | |
41 <inputs> | |
42 <conditional name="formatType"> | |
43 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
44 <option value="bed">bed</option> | |
45 <option value="gff">gff</option> | |
46 <option value="gff2">gff2</option> | |
47 <option value="gff3">gff3</option> | |
48 <option value="sam">sam</option> | |
49 <option value="gtf">gtf</option> | |
50 </param> | |
51 <when value="bed"> | |
52 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
53 </when> | |
54 <when value="gff"> | |
55 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
56 </when> | |
57 <when value="gff2"> | |
58 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
59 </when> | |
60 <when value="gff3"> | |
61 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
62 </when> | |
63 <when value="sam"> | |
64 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
65 </when> | |
66 <when value="gtf"> | |
67 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
68 </when> | |
69 </conditional> | |
70 | |
71 <conditional name="OptionStart"> | |
72 <param name="start" type="select" label="shrink to the start of the feature"> | |
73 <option value="Yes">Yes</option> | |
74 <option value="No" selected="true">No</option> | |
75 </param> | |
76 <when value="Yes"> | |
77 <param name="startValue" type="integer" value="0"/> | |
78 </when> | |
79 <when value="No"> | |
80 </when> | |
81 </conditional> | |
82 | |
83 <conditional name="OptionEnd"> | |
84 <param name="end" type="select" label="shrink to the end of the feature"> | |
85 <option value="Yes">Yes</option> | |
86 <option value="No" selected="true">No</option> | |
87 </param> | |
88 <when value="Yes"> | |
89 <param name="endValue" type="integer" value="0"/> | |
90 </when> | |
91 <when value="No"> | |
92 </when> | |
93 </conditional> | |
94 | |
95 | |
96 <conditional name="OptionFivePrim"> | |
97 <param name="five" type="select" label="extend to the 5' direction"> | |
98 <option value="Yes">Yes</option> | |
99 <option value="No" selected="true">No</option> | |
100 </param> | |
101 <when value="Yes"> | |
102 <param name="fivePValue" type="integer" value="0"/> | |
103 </when> | |
104 <when value="No"> | |
105 </when> | |
106 </conditional> | |
107 | |
108 <conditional name="OptionTroisP"> | |
109 <param name="TroisP" type="select" label="extend to the 3' direction"> | |
110 <option value="Yes">Yes</option> | |
111 <option value="No" selected="true">No</option> | |
112 </param> | |
113 <when value="Yes"> | |
114 <param name="ThreePValue" type="integer" value="0"/> | |
115 </when> | |
116 <when value="No"> | |
117 </when> | |
118 </conditional> | |
119 | |
120 | |
121 </inputs> | |
122 | |
123 <outputs> | |
124 <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/> | |
125 </outputs> | |
126 | |
127 <help> | |
128 This tool reads a list of transcripts and modifies each feature by: | |
129 | |
130 - shrinking it to the *n* first nucleotides or the *n* last nucleotides, or | |
131 | |
132 - extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream). | |
133 | |
134 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!). | |
135 | |
136 The tool needs a transcript file, its format, and outputs a new transcript file. | |
137 </help> | |
138 </tool> |