Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/getDifference.xml @ 36:44d5973c188c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
parents
children
comparison
equal deleted inserted replaced
35:d94018ca4ada 36:44d5973c188c
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 <command interpreter="python">
4 ../Java/Python/getDifference.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName1 == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName1 == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName1 == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName1 == 'gtf':
16 -f gtf
17 #end if
18
19 -j $formatType2.inputFileName2
20 #if $formatType2.FormatInputFileName2 == 'bed':
21 -g bed
22 #elif $formatType2.FormatInputFileName2 == 'gff':
23 -g gff
24 #elif $formatType2.FormatInputFileName2 == 'gff2':
25 -g gff2
26 #elif $formatType2.FormatInputFileName2 == 'gff3':
27 -g gff3
28 #elif $formatType2.FormatInputFileName2 == 'sam':
29 -g sam
30 #elif $formatType2.FormatInputFileName2 == 'gtf':
31 -g gtf
32 #end if
33
34 $split
35
36 #if $OptionSequence.option == "Yes":
37 -s $OptionSequence.sequence
38 #end if
39
40 -o $outputFileGff
41
42
43 </command>
44
45 <inputs>
46 <conditional name="formatType">
47 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
48 <option value="bed">bed</option>
49 <option value="gff">gff</option>
50 <option value="gff2">gff2</option>
51 <option value="gff3">gff3</option>
52 <option value="sam">sam</option>
53 <option value="gtf">gtf</option>
54 </param>
55 <when value="bed">
56 <param name="inputFileName1" format="bed" type="data" label="Input File "/>
57 </when>
58 <when value="gff">
59 <param name="inputFileName1" format="gff" type="data" label="Input File "/>
60 </when>
61 <when value="gff2">
62 <param name="inputFileName1" format="gff2" type="data" label="Input File "/>
63 </when>
64 <when value="gff3">
65 <param name="inputFileName1" format="gff3" type="data" label="Input File "/>
66 </when>
67 <when value="sam">
68 <param name="inputFileName1" format="sam" type="data" label="Input File "/>
69 </when>
70 <when value="gtf">
71 <param name="inputFileName1" format="gtf" type="data" label="Input File "/>
72 </when>
73 </conditional>
74
75 <conditional name="formatType2">
76 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
77 <option value="bed">bed</option>
78 <option value="gff">gff</option>
79 <option value="gff2">gff2</option>
80 <option value="gff3">gff3</option>
81 <option value="sam">sam</option>
82 <option value="gtf">gtf</option>
83 </param>
84 <when value="bed">
85 <param name="inputFileName2" format="bed" type="data" label="reference file"/>
86 </when>
87 <when value="gff">
88 <param name="inputFileName2" format="gff" type="data" label="reference file"/>
89 </when>
90 <when value="gff2">
91 <param name="inputFileName2" format="gff2" type="data" label="reference file"/>
92 </when>
93 <when value="gff3">
94 <param name="inputFileName2" format="gff3" type="data" label="reference file"/>
95 </when>
96 <when value="sam">
97 <param name="inputFileName2" format="sam" type="data" label="reference file"/>
98 </when>
99 <when value="gtf">
100 <param name="inputFileName2" format="gtf" type="data" label="reference file"/>
101 </when>
102 </conditional>
103
104 <param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="When comparing to a set of genomic coordinates, do not join into exons."/>
105
106 <conditional name="OptionSequence">
107 <param name="option" type="select" label="Compare with a reference fasta file.">
108 <option value="Yes">Yes</option>
109 <option value="No" selected="true">No</option>
110 </param>
111 <when value="Yes">
112 <param name="sequence" type="data" label="Fasta File" format="fasta"/>
113 </when>
114 <when value="No">
115 </when>
116 </conditional>
117
118 </inputs>
119
120
121 <outputs>
122 <data name="outputFileGff" format="gff3" label="[getDifference]output File."/>
123 </outputs>
124
125 <help>
126 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.
127
128 When only one set of transcripts is given, together with a reference genome, it produces a list of transcripts which complements the first set.
129 </help>
130 </tool>