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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:52:49 -0400
parents 1bc76ceffa7f
children
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3:0926c81f382c 4:381cd27bf67a
1 <tool id="gops_merge_1" name="Merge" version="1.0.0"> 1 <tool id="gops_merge_1" name="Merge" version="1.0.0">
2 <description>the overlapping intervals of a dataset</description> 2 <description>the overlapping intervals of a dataset</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command> 7 <code file="operation_filter.py">
8 <inputs> 8 <hook exec_after_process="exec_after_merge" />
9 <param format="interval" name="input1" type="data"> 9 </code>
10 <label>Merge overlaping regions of</label> 10 <command><![CDATA[
11 </param> 11 python '$__tool_directory__/gops_merge.py'
12 <param name="returntype" type="boolean" truevalue="-3" falsevalue=""> 12 '$input1'
13 <label>Output 3 column bed</label> 13 '$output'
14 </param> 14 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
15 </inputs> 15 $returntype
16 <outputs> 16 ]]></command>
17 <data format="input" name="output" metadata_source="input1" /> 17 <inputs>
18 </outputs> 18 <param name="input1" type="data" format="interval" label="Merge overlapping regions of" />
19 <code file="operation_filter.py"> 19 <param name="returntype" type="boolean" truevalue="-3" falsevalue="" label="Output 3 column bed" />
20 <hook exec_after_process="exec_after_merge" /> 20 </inputs>
21 </code> 21 <outputs>
22 <tests> 22 <data name="output" format_source="input1" metadata_source="input1" />
23 <test> 23 </outputs>
24 <param name="input1" value="1.bed" /> 24 <tests>
25 <output name="output" file="gops-merge.dat" /> 25 <test>
26 <param name="returntype" value="true" /> 26 <param name="input1" value="1.bed" />
27 </test> 27 <param name="returntype" value="true" />
28 <test> 28 <output name="output" file="gops-merge.dat" />
29 <param name="input1" value="2_mod.bed" ftype="interval"/> 29 </test>
30 <output name="output" file="gops_merge_diffCols.dat" /> 30 <test>
31 <param name="returntype" value="true" /> 31 <param name="input1" value="2_mod.bed" ftype="interval"/>
32 </test> 32 <param name="returntype" value="true" />
33 <test> 33 <output name="output" file="gops_merge_diffCols.dat" />
34 <param name="input1" value="gops_bigint.interval" /> 34 </test>
35 <output name="output" file="gops_merge_out2.bed" /> 35 <test>
36 <param name="returntype" value="true" /> 36 <param name="input1" value="gops_bigint.interval" />
37 </test> 37 <param name="returntype" value="true" />
38 </tests> 38 <output name="output" file="gops_merge_out2.bed" />
39 <help> 39 </test>
40 40 </tests>
41 <help><![CDATA[
41 .. class:: infomark 42 .. class:: infomark
42 43
43 **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. 44 **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.
44 45
45 ----- 46 @SCREENCASTS@
46
47 **Screencasts!**
48
49 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
50
51 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
52
53 -----
54 47
55 This operation merges all overlapping intervals into single intervals. 48 This operation merges all overlapping intervals into single intervals.
56 49
57 **Example** 50 **Example**
58 51
59 .. image:: gops_merge.gif 52 .. image:: gops_merge.gif
60 53 ]]></help>
61 </help>
62 </tool> 54 </tool>