Mercurial > repos > iuc > crossmap_bw
comparison crossmap_bigwig.xml @ 3:f208825f64ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author | iuc |
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date | Thu, 24 May 2018 19:10:13 -0400 |
parents | 566f43df9ef4 |
children | a6d677dbf019 |
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2:566f43df9ef4 | 3:f208825f64ec |
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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> |