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comparison crossmap_bigwig.xml @ 4:bbd9d5b629f2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:08:23 -0400
parents d3051afe9a38
children cafcf7eecf44
comparison
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3:d3051afe9a38 4:bbd9d5b629f2
1 <tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@-0"> 1 <tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description> 2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
9 9
10 <command><![CDATA[ 10 <command><![CDATA[
11 CrossMap.py bigwig 11 CrossMap.py bigwig
12 '${chain_source.input_chain}' 12 '${chain_source.input_chain}'
13 '${input}' 13 '${input}'
14 '${output}' 14 output
15
16 && mv '${output}.bw' '${output}'
17 ]]></command> 15 ]]></command>
18 16
19 <inputs> 17 <inputs>
20 <param name="input" type="data" format="bigwig" label="BigWig file"/> 18 <param name="input" type="data" format="bigwig" label="BigWig file"/>
21 19
22 <expand macro="chain" /> 20 <expand macro="chain" />
23 </inputs> 21 </inputs>
24 22
25 <outputs> 23 <outputs>
26 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" /> 24 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
27 </outputs> 25 </outputs>
28 26
29 <tests> 27 <tests>
30 <test> 28 <test>
31 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/> 29 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
52 the input, the output will always in bedGraph format. bedGraph format is 50 the input, the output will always in bedGraph format. bedGraph format is
53 similar to wiggle format and can be converted into BigWig format using UCSC 51 similar to wiggle format and can be converted into BigWig format using UCSC
54 wigToBigWig tool. We export files in bedGraph because it is usually much 52 wigToBigWig tool. We export files in bedGraph because it is usually much
55 smaller than file in wiggle format, and more importantly, CrossMap 53 smaller than file in wiggle format, and more importantly, CrossMap
56 internally transforms wiggle into bedGraph to increase running speed. 54 internally transforms wiggle into bedGraph to increase running speed.
57
58 ]]></help> 55 ]]></help>
59 56
60 <citations> 57 <citations>
61 <citation type="doi">10.1093/bioinformatics/btt730</citation> 58 <citation type="doi">10.1093/bioinformatics/btt730</citation>
62 </citations> 59 </citations>