Mercurial > repos > iuc > crossmap_wig
comparison crossmap_wig.xml @ 3:8c26026e7ad9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author | iuc |
---|---|
date | Thu, 24 May 2018 19:10:34 -0400 |
parents | d0e7cc22351f |
children | 282a658c6569 |
comparison
equal
deleted
inserted
replaced
2:d0e7cc22351f | 3:8c26026e7ad9 |
---|---|
1 <tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@-0"> | 1 <tool id="crossmap_wig" name="CrossMap Wig" 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"/> |
8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
9 <command><![CDATA[ | 9 <command><![CDATA[ |
10 CrossMap.py wig | 10 CrossMap.py wig |
11 '${chain_source.input_chain}' | 11 '${chain_source.input_chain}' |
12 '${input}' | 12 '${input}' |
13 '${output}' | 13 output |
14 | |
15 && mv '${output}.bw' '${output}' | |
16 && mv '${output}.sorted.bgr' '${output2}' | |
17 ]]></command> | 14 ]]></command> |
18 | 15 |
19 <inputs> | 16 <inputs> |
20 <param name="input" type="data" format="wig" label="Wiggle file"/> | 17 <param name="input" type="data" format="wig" label="Wiggle file"/> |
21 | 18 |
22 <expand macro="chain" /> | 19 <expand macro="chain" /> |
23 </inputs> | 20 </inputs> |
24 | 21 |
25 <outputs> | 22 <outputs> |
26 <data name="output" format="wig" label="${tool.name} on ${on_string}" /> | 23 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" /> |
27 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" /> | 24 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" /> |
28 </outputs> | 25 </outputs> |
29 | 26 |
30 <tests> | 27 <tests> |
31 <!-- WIG - Doesn't understand fixedStep --> | 28 <!-- WIG - Doesn't understand fixedStep --> |
32 <test> | 29 <test> |
57 the input, the output will always in bedGraph format. bedGraph format is | 54 the input, the output will always in bedGraph format. bedGraph format is |
58 similar to wiggle format and can be converted into BigWig format using UCSC | 55 similar to wiggle format and can be converted into BigWig format using UCSC |
59 wigToBigWig tool. We export files in bedGraph because it is usually much | 56 wigToBigWig tool. We export files in bedGraph because it is usually much |
60 smaller than file in wiggle format, and more importantly, CrossMap | 57 smaller than file in wiggle format, and more importantly, CrossMap |
61 internally transforms wiggle into bedGraph to increase running speed. | 58 internally transforms wiggle into bedGraph to increase running speed. |
62 | |
63 ]]></help> | 59 ]]></help> |
64 | 60 |
65 <citations> | 61 <citations> |
66 <citation type="doi">10.1093/bioinformatics/btt730</citation> | 62 <citation type="doi">10.1093/bioinformatics/btt730</citation> |
67 </citations> | 63 </citations> |