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comparison crossmap_bigwig.xml @ 0:143ec4d1c8f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
author iuc
date Tue, 26 Sep 2017 05:45:25 -0400
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children 3b82b6febfd3
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-1:000000000000 0:143ec4d1c8f3
1 <tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@-0">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9
10 <command><![CDATA[
11 #set $input_file = str($seq_source.input)
12
13 CrossMap.py bigwig
14 '${chain_source.input_chain}'
15 '${input_file}'
16 '${output}'
17
18 && mv '${output}.bw' '${output}'
19
20 ]]></command>
21
22 <inputs>
23 <conditional name="seq_source">
24 <expand macro="source" />
25 <when value="cached">
26 <param format="bigwig" name="input" type="data" label="BigWig file">
27 <validator type="unspecified_build"/>
28 <!-- Gives error in tests
29 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
30 -->
31 </param>
32 </when>
33 <when value="history">
34 <param type="data" format="bigwig" name="input" label="BigWig file"/>
35 </when>
36 </conditional>
37 <expand macro="chain" />
38 </inputs>
39
40 <outputs>
41 <data format="bigwig" name="output" label="${tool.name} on ${on_string}" />
42 </outputs>
43
44 <tests>
45 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
46 <test>
47 <param name="input_format" value="bigwig"/>
48 <param name="index_source" value="history"/>
49 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
50 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
51 <param name="include_fails" value="False"/>
52
53 <output name="output" file="test_bigwig_01_output_a.bw"/>
54 </test>
55 </tests>
56 <help><![CDATA[
57 @HELP_GENERAL@
58
59 BigWig
60 ------
61
62 Input wiggle data can be in variableStep (for data with irregular
63 intervals) or fixedStep (for data with regular intervals). Regardless of
64 the input, the output will always in bedGraph format. bedGraph format is
65 similar to wiggle format and can be converted into BigWig format using UCSC
66 wigToBigWig tool. We export files in bedGraph because it is usually much
67 smaller than file in wiggle format, and more importantly, CrossMap
68 internally transforms wiggle into bedGraph to increase running speed.
69
70 Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details
71 ]]></help>
72
73 <citations>
74 <citation type="doi">10.1093/bioinformatics/btt730</citation>
75 </citations>
76 </tool>