Mercurial > repos > devteam > subtract

annotate subtract.xml @ 5:0145969324c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:53:03 -0400
parents ecb36112b056
children
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">
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
2 <description>the intervals of two datasets</description>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
3 <macros>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
4 <import>macros.xml</import>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
5 </macros>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
6 <expand macro="requirements" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
7 <code file="operation_filter.py"/>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
8 <command><![CDATA[
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
9 python '$__tool_directory__/gops_subtract.py'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
10 '$input1'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
11 '$input2'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
12 '$output'
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
13
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
14 #if $input1.is_of_type('gff')
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
15 -1 1,4,5,7 --gff1
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
16 #else:
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
17 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
18 #end if
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
19
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
20 #if $input2.is_of_type('gff')
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
21 -2 1,4,5,7 --gff2
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
22 #else:
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
23 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
24 #end if
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
25
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
26 -m $min
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
27 $returntype
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
28 ]]></command>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
29 <inputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
30 <param name="input2" type="data" format="interval,gff" label="Subtract" help="Second dataset" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
31 <param name="input1" type="data" format="interval,gff" label="from" help="First dataset" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
32 <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
33 <option value="">Intervals with no overlap</option>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
34 <option value="-p">Non-overlapping pieces of intervals</option>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
35 </param>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
36 <param name="min" type="integer" value="1" min="1" label="where minimal overlap is" help="(bp)" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
37 </inputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
38 <outputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
39 <data name="output" format_source="input1" metadata_source="input1"/>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
40 </outputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
41 <tests>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
42 <test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
43 <param name="input1" value="1.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
44 <param name="input2" value="2.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
45 <param name="min" value="1" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
46 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
47 <output name="output" file="gops-subtract.dat" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
48 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
49 <test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
50 <param name="input1" value="1.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
51 <param name="input2" value="2_mod.bed" ftype="interval"/>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
52 <param name="min" value="1" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
53 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
54 <output name="output" file="gops_subtract_diffCols.dat" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
55 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
56 <test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
57 <param name="input1" value="gops_subtract_bigint.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
58 <param name="input2" value="2.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
59 <param name="min" value="1" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
60 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
61 <output name="output" file="gops-subtract.dat" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
62 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
63 <test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
64 <param name="input1" value="1.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
65 <param name="input2" value="2.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
66 <param name="min" value="10" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
67 <param name="returntype" value="Non-overlapping pieces of intervals" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
68 <output name="output" file="gops-subtract-p.dat" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
69 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
70 <!-- Subtract two GFF files. -->
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
71 <test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
72 <param name="input1" value="gops_subtract_in1.gff" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
73 <param name="input2" value="gops_subtract_in2.gff" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
74 <param name="min" value="1" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
75 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
76 <output name="output" file="gops_subtract_out1.gff" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
77 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
78 <!-- Subtract BED file from GFF file. -->
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
79 <test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
80 <param name="input1" value="gops_subtract_in1.gff" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
81 <param name="input2" value="gops_subtract_in2.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
82 <param name="min" value="1" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
83 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
84 <output name="output" file="gops_subtract_out1.gff" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
85 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
86 </tests>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
87 <help><![CDATA[
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
88 .. class:: infomark
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
89
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
90 **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
91
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
92 @SCREENCASTS@
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
93
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
94 **Syntax**
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
95
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
96 - **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
97 - **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
98 - **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
99
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
100 -----
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
101
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
102 **Example**
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
103
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
104 Intervals with no overlap:
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
105
2
c19a2a29c561 Added tool images.
devteam <devteam@galaxyproject.org>
parents: 1
diff changeset
106 .. image:: gops_subtractOverlappingIntervals.gif
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
107
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
108 Non-overlapping pieces of intervals:
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
109
2
c19a2a29c561 Added tool images.
devteam <devteam@galaxyproject.org>
parents: 1
diff changeset
110 .. image:: gops_subtractOverlappingPieces.gif
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 3
diff changeset
111 ]]></help>
0
5bc2dacbe729 Imported from capsule None
devteam
parents:
diff changeset
112 </tool>