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comparison crossmap_bigwig.xml @ 10:d183effe8199 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 11:59:11 +0000
parents cafcf7eecf44
children
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9:c1a0f42d6c2a 10:d183effe8199
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9
10 <command><![CDATA[ 9 <command><![CDATA[
11 CrossMap.py bigwig 10 CrossMap bigwig
12 '${chain_source.input_chain}' 11 '${chain_source.input_chain}'
13 '${input}' 12 '${input}'
14 output 13 output
15 ]]></command> 14 ]]></command>
16
17 <inputs> 15 <inputs>
18 <param name="input" type="data" format="bigwig" label="BigWig file"/> 16 <param name="input" type="data" format="bigwig" label="BigWig file"/>
19 17 <expand macro="chain"/>
20 <expand macro="chain" />
21 </inputs> 18 </inputs>
22
23 <outputs> 19 <outputs>
24 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" /> 20 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw"/>
25 </outputs> 21 </outputs>
26
27 <tests> 22 <tests>
28 <test> 23 <test>
29 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/> 24 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
30 <param name="index_source" value="history"/> 25 <param name="index_source" value="history"/>
31 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 26 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
32
33 <output name="output" file="test_bigwig_01_output_a.bw"/> 27 <output name="output" file="test_bigwig_01_output_a.bw"/>
34 </test> 28 </test>
35 <test><!-- cached chain file --> 29 <test>
30 <!-- cached chain file -->
36 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig" dbkey="hg18"/> 31 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig" dbkey="hg18"/>
37 <param name="index_source" value="cached"/> 32 <param name="index_source" value="cached"/>
38
39 <output name="output" file="test_bigwig_01_output_a.bw"/> 33 <output name="output" file="test_bigwig_01_output_a.bw"/>
40 </test> 34 </test>
41 </tests> 35 </tests>
42 <help><![CDATA[ 36 <help><![CDATA[
43 @HELP_GENERAL@ 37 @HELP_GENERAL@
51 similar to wiggle format and can be converted into BigWig format using UCSC 45 similar to wiggle format and can be converted into BigWig format using UCSC
52 wigToBigWig tool. We export files in bedGraph because it is usually much 46 wigToBigWig tool. We export files in bedGraph because it is usually much
53 smaller than file in wiggle format, and more importantly, CrossMap 47 smaller than file in wiggle format, and more importantly, CrossMap
54 internally transforms wiggle into bedGraph to increase running speed. 48 internally transforms wiggle into bedGraph to increase running speed.
55 ]]></help> 49 ]]></help>
56
57 <citations> 50 <citations>
58 <citation type="doi">10.1093/bioinformatics/btt730</citation> 51 <citation type="doi">10.1093/bioinformatics/btt730</citation>
59 </citations> 52 </citations>
60 </tool> 53 </tool>