annotate SMART/galaxy/mergeTranscriptLists.xml @ 9:1eb55963fe39

Updated CompareOverlappingSmall*.py
author m-zytnicki
date Thu, 14 Mar 2013 05:23:05 -0400
parents 769e306b7933
children 440ceca58672
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 <tool id="mergeTranscriptLists" name="merge transcript lists">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 <description>Merge the elements of two lists of genomic coordinates.</description>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 <command interpreter="python">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 #if $formatType.FormatInputFileName1 == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 -f bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 #elif $formatType.FormatInputFileName1 == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 #elif $formatType.FormatInputFileName1 == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 #elif $formatType.FormatInputFileName1 == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 #elif $formatType.FormatInputFileName1 == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 -f sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 #elif $formatType.FormatInputFileName1 == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 -f gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 -j $formatType2.inputFileName2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 #if $formatType2.FormatInputFileName2 == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 -g bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 #elif $formatType2.FormatInputFileName2 == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 -g gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 #elif $formatType2.FormatInputFileName2 == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 -g gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 #elif $formatType2.FormatInputFileName2 == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 -g gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 #elif $formatType2.FormatInputFileName2 == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 -g sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 #elif $formatType2.FormatInputFileName2 == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 -g gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 $all
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 $normalize
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 #if $OptionDistance.dis == 'Yes':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 -d $OptionDistance.disVal
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 -c
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 -a
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 -o $outputFileGff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 <conditional name="formatType2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
89 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
92 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
93 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
94 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
95 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
96 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
97 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
98 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
99 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
100 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
101 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
102 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
103 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
104 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
105 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
106 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
107 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
108 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
109 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
110 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
111
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
112
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
113 <param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
114 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
115
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
116 <conditional name="OptionDistance">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
117 <param name="dis" type="select" label="provide the number of reads" >
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
118 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
119 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
120 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
121 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
122 <param name="disVal" type="integer" value="0" label="max. distance between two transcripts" />
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
123 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
124 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
125 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
126 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
127
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
128 <conditional name="OptionColinearOrAntiSens">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
129 <param name="OptionCA" type="select" label="Colinear or anti-sens">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
130 <option value="Colinear">Colinear</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
131 <option value="AntiSens">AntiSens</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
132 <option value="NONE" selected="true">NONE</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
133 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
134 <when value="Colinear">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
135 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
136 <when value="AntiSens">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
137 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
138 <when value="NONE">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
139 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
140 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
141
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
142 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
143
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
144 <outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
145 <data name="outputFileGff" format="gff3" label="[mergeTranscriptLists]out file"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
146 </outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
147
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
148 </tool>