annotate subtract.xml @ 1:7bf44b9d7a8b

Corrected version string.
author devteam <devteam@galaxyproject.org>
date Thu, 10 Apr 2014 13:47:31 -0400
parents 5bc2dacbe729
children c19a2a29c561
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
7bf44b9d7a8b Corrected version string.
devteam <devteam@galaxyproject.org>
parents: 0
diff changeset
1 <tool id="gops_subtract_1" name="Subtract" version="1.0.0">
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
2 <description>the intervals of two datasets</description>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
3 <requirements>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
4 <requirement type="package" version="0.7.1">bx-python</requirement>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
6 </requirements>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
7 <command interpreter="python">gops_subtract.py
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
8 $input1 $input2 $output
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
9
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
10 #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
11 -1 1,4,5,7 --gff1
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
12 #else:
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
14 #end if
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
15
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
16 #if isinstance( $input2.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
17 -2 1,4,5,7 --gff2
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
18 #else:
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
19 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
20 #end if
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
21
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
22 -m $min $returntype
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
23 </command>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
24 <inputs>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
25 <param format="interval,gff" name="input2" type="data" help="Second dataset">
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
26 <label>Subtract</label>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
27 </param>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
28
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
29 <param format="interval,gff" name="input1" type="data" help="First dataset">
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
30 <label>from</label>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
31 </param>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
32
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
33 <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
34 <option value="">Intervals with no overlap</option>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
35 <option value="-p">Non-overlapping pieces of intervals</option>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
36 </param>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
37
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
38 <param name="min" size="4" type="integer" value="1" min="1" help="(bp)">
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
39 <label>where minimal overlap is</label>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
40 </param>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
41 </inputs>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
42 <outputs>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
43 <data format="input" name="output" metadata_source="input1"/>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
44 </outputs>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
45 <code file="operation_filter.py"/>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
46 <trackster_conf/>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
47 <tests>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
48 <test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
49 <param name="input1" value="1.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
50 <param name="input2" value="2.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
51 <param name="min" value="1" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
52 <param name="returntype" value="" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
53 <output name="output" file="gops-subtract.dat" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
54 </test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
55 <test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
56 <param name="input1" value="1.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
57 <param name="input2" value="2_mod.bed" ftype="interval"/>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
58 <param name="min" value="1" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
59 <param name="returntype" value="" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
60 <output name="output" file="gops_subtract_diffCols.dat" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
61 </test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
62 <test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
63 <param name="input1" value="gops_subtract_bigint.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
64 <param name="input2" value="2.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
65 <param name="min" value="1" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
66 <param name="returntype" value="" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
67 <output name="output" file="gops-subtract.dat" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
68 </test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
69 <test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
70 <param name="input1" value="1.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
71 <param name="input2" value="2.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
72 <param name="min" value="10" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
73 <param name="returntype" value="Non-overlapping pieces of intervals" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
74 <output name="output" file="gops-subtract-p.dat" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
75 </test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
76 <!-- Subtract two GFF files. -->
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
77 <test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
78 <param name="input1" value="gops_subtract_in1.gff" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
79 <param name="input2" value="gops_subtract_in2.gff" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
80 <param name="min" value="1" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
81 <param name="returntype" value="" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
82 <output name="output" file="gops_subtract_out1.gff" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
83 </test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
84 <!-- Subtract BED file from GFF file. -->
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
85 <test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
86 <param name="input1" value="gops_subtract_in1.gff" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
87 <param name="input2" value="gops_subtract_in2.bed" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
88 <param name="min" value="1" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
89 <param name="returntype" value="" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
90 <output name="output" file="gops_subtract_out1.gff" />
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
91 </test>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
92 </tests>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
93 <help>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
94
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
95 .. class:: infomark
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
96
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
97 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
98
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
99 -----
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
100
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
101 **Screencasts!**
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
102
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
103 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
104
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
105 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
106
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
107 -----
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
108
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
109 **Syntax**
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
110
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
111 - **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two datasets.
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
112 - **Intervals with no overlap** returns entire intervals from the first dataset that do not overlap the second dataset. The returned intervals are completely unchanged, and this option only filters out intervals that overlap with the second dataset.
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
113 - **Non-overlapping pieces of intervals** returns intervals from the first dataset that have the intervals from the second dataset removed. Any overlapping base pairs are removed from the range of the interval. All fields besides start and end are guaranteed to remain unchanged.
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
114
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
115 -----
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
116
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
117 **Example**
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
118
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
119 Intervals with no overlap:
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
120
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
121 .. image:: ${static_path}/operation_icons/gops_subtractOverlappingIntervals.gif
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
122
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
123 Non-overlapping pieces of intervals:
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
124
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
125 .. image:: ${static_path}/operation_icons/gops_subtractOverlappingPieces.gif
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
126
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
127 </help>
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
128 </tool>