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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:29 -0400
parents 4cd116158aef
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1 <tool id="get_flanks1" name="Get flanks" version="1.0.0"> 1 <tool id="get_flanks1" name="Get flanks" version="1.0.0">
2 <description>returns flanking region/s for every gene</description> 2 <description>returns flanking region/s for every gene</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">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command> 7 <command><![CDATA[
8 <inputs> 8 python '$__tool_directory__/get_flanks.py'
9 <param format="interval" name="input" type="data" label="Select data"/> 9 '$input'
10 <param name="region" type="select" label="Region"> 10 '$out_file1'
11 <option value="whole" selected="true">Whole feature</option> 11 $size
12 <option value="start">Around Start</option> 12 $direction
13 <option value="end">Around End</option> 13 $region
14 </param> 14 -o $offset
15 <param name="direction" type="select" label="Location of the flanking region/s"> 15 -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
16 <option value="Upstream">Upstream</option> 16 ]]></command>
17 <option value="Downstream">Downstream</option> 17 <inputs>
18 <option value="Both">Both</option> 18 <param name="input" type="data" format="interval" label="Select data"/>
19 </param> 19 <param name="region" type="select" label="Region">
20 <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/> 20 <option value="whole" selected="true">Whole feature</option>
21 <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/> 21 <option value="start">Around Start</option>
22 22 <option value="end">Around End</option>
23 23 </param>
24 </inputs> 24 <param name="direction" type="select" label="Location of the flanking region/s">
25 <outputs> 25 <option value="Upstream">Upstream</option>
26 <data format="interval" name="out_file1" metadata_source="input"/> 26 <option value="Downstream">Downstream</option>
27 </outputs> 27 <option value="Both">Both</option>
28 <tests> 28 </param>
29 <test> 29 <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
30 <param name="input" value="flanks_inp.bed"/> 30 <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
31 <param name="offset" value="-500"/> 31 </inputs>
32 <param name="size" value="1000"/> 32 <outputs>
33 <param name="direction" value="Both"/> 33 <data name="out_file1" format_source="input" metadata_source="input"/>
34 <param name="region" value="whole"/> 34 </outputs>
35 <output name="out_file1" file="flanks_out1.bed"/> 35 <tests>
36 </test> 36 <test>
37 <test> 37 <param name="input" value="flanks_inp.bed"/>
38 <param name="input" value="flanks_inp.bed"/> 38 <param name="offset" value="-500"/>
39 <param name="offset" value="200"/> 39 <param name="size" value="1000"/>
40 <param name="size" value="1000"/> 40 <param name="direction" value="Both"/>
41 <param name="direction" value="Downstream"/> 41 <param name="region" value="whole"/>
42 <param name="region" value="start" /> 42 <output name="out_file1" file="flanks_out1.bed"/>
43 <output name="out_file1" file="flanks_out2.bed"/> 43 </test>
44 </test> 44 <test>
45 </tests> 45 <param name="input" value="flanks_inp.bed"/>
46 <help> 46 <param name="offset" value="200"/>
47 47 <param name="size" value="1000"/>
48 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. 48 <param name="direction" value="Downstream"/>
49 <param name="region" value="start" />
50 <output name="out_file1" file="flanks_out2.bed"/>
51 </test>
52 </tests>
53 <help><![CDATA[
54 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
49 55
50 **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue". 56 **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
51 57
52 ----- 58 -----
53
54 59
55 **Example 1** 60 **Example 1**
56 61
57 - For the following dataset:: 62 - For the following dataset::
58 63
73 - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**:: 78 - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::
74 79
75 chr22 500 800 NM_028946 0 - 80 chr22 500 800 NM_028946 0 -
76 81
77 .. image:: flanks_ex2.gif 82 .. image:: flanks_ex2.gif
78 83 ]]></help>
79 </help>
80
81
82 </tool> 84 </tool>