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comparison SMART/galaxy/getDifference.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="getDifference" name="get difference">
2 <description>Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/getDifference.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName1 == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName1 == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName1 == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName1 == 'gtf':
19 -f gtf
20 #end if
21
22 -j $formatType2.inputFileName2
23 #if $formatType2.FormatInputFileName2 == 'bed':
24 -g bed
25 #elif $formatType2.FormatInputFileName2 == 'gff':
26 -g gff
27 #elif $formatType2.FormatInputFileName2 == 'gff2':
28 -g gff2
29 #elif $formatType2.FormatInputFileName2 == 'gff3':
30 -g gff3
31 #elif $formatType2.FormatInputFileName2 == 'sam':
32 -g sam
33 #elif $formatType2.FormatInputFileName2 == 'gtf':
34 -g gtf
35 #end if
36
37 $split
38
39 #if $OptionSequence.option == "Yes":
40 -s $OptionSequence.sequence
41 #end if
42
43 -o $outputFileGff
44
45
46 </command>
47
48 <inputs>
49 <conditional name="formatType">
50 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
51 <option value="bed">bed</option>
52 <option value="gff">gff</option>
53 <option value="gff2">gff2</option>
54 <option value="gff3">gff3</option>
55 <option value="sam">sam</option>
56 <option value="gtf">gtf</option>
57 </param>
58 <when value="bed">
59 <param name="inputFileName1" format="bed" type="data" label="Input File "/>
60 </when>
61 <when value="gff">
62 <param name="inputFileName1" format="gff" type="data" label="Input File "/>
63 </when>
64 <when value="gff2">
65 <param name="inputFileName1" format="gff2" type="data" label="Input File "/>
66 </when>
67 <when value="gff3">
68 <param name="inputFileName1" format="gff3" type="data" label="Input File "/>
69 </when>
70 <when value="sam">
71 <param name="inputFileName1" format="sam" type="data" label="Input File "/>
72 </when>
73 <when value="gtf">
74 <param name="inputFileName1" format="gtf" type="data" label="Input File "/>
75 </when>
76 </conditional>
77
78 <conditional name="formatType2">
79 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
80 <option value="bed">bed</option>
81 <option value="gff">gff</option>
82 <option value="gff2">gff2</option>
83 <option value="gff3">gff3</option>
84 <option value="sam">sam</option>
85 <option value="gtf">gtf</option>
86 </param>
87 <when value="bed">
88 <param name="inputFileName2" format="bed" type="data" label="reference file"/>
89 </when>
90 <when value="gff">
91 <param name="inputFileName2" format="gff" type="data" label="reference file"/>
92 </when>
93 <when value="gff2">
94 <param name="inputFileName2" format="gff2" type="data" label="reference file"/>
95 </when>
96 <when value="gff3">
97 <param name="inputFileName2" format="gff3" type="data" label="reference file"/>
98 </when>
99 <when value="sam">
100 <param name="inputFileName2" format="sam" type="data" label="reference file"/>
101 </when>
102 <when value="gtf">
103 <param name="inputFileName2" format="gtf" type="data" label="reference file"/>
104 </when>
105 </conditional>
106
107 <param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="When comparing to a set of genomic coordinates, do not join into exons."/>
108
109 <conditional name="OptionSequence">
110 <param name="option" type="select" label="Compare with a reference fasta file.">
111 <option value="Yes">Yes</option>
112 <option value="No" selected="true">No</option>
113 </param>
114 <when value="Yes">
115 <param name="sequence" type="data" label="Fasta File" format="fasta"/>
116 </when>
117 <when value="No">
118 </when>
119 </conditional>
120
121 </inputs>
122
123
124 <outputs>
125 <data name="outputFileGff" format="gff3" label="[get difference] output file."/>
126 </outputs>
127
128 <help>
129 This tools has two different (but similar) uses. When given two sets of transcripts, it trims the elements of the set so that they do not overlap with the second set.
130
131 When only one set of transcripts is given, together with a reference genome, it produces a list of transcripts which complements the first set.
132 </help>
133 </tool>