Mercurial > repos > iuc > crossmap_wig

comparison crossmap_wig.xml @ 9:f7229c8445da 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 12:01:52 +0000
parents 282a658c6569
children
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8:e72c320c17c1 9:f7229c8445da
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 <command><![CDATA[ 9 <command><![CDATA[
10 CrossMap.py wig 10 CrossMap wig
11 '${chain_source.input_chain}' 11 '${chain_source.input_chain}'
12 '${input}' 12 '${input}'
13 output 13 output
14 ]]></command> 14 ]]></command>
15
16 <inputs> 15 <inputs>
17 <param name="input" type="data" format="wig" label="Wiggle file"/> 16 <param name="input" type="data" format="wig" label="Wiggle file"/>
18 17 <expand macro="chain"/>
19 <expand macro="chain" />
20 </inputs> 18 </inputs>
21
22 <outputs> 19 <outputs>
23 <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 ${on_string}" from_work_dir="output.bw"/>
24 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" /> 21 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr"/>
25 </outputs> 22 </outputs>
26
27 <tests> 23 <tests>
28 <!-- WIG - Doesn't understand fixedStep --> 24 <!-- WIG - Doesn't understand fixedStep -->
29 <test> 25 <test>
30 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> 26 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
31 <param name="index_source" value="history"/> 27 <param name="index_source" value="history"/>
32 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 28 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
33
34 <output name="output" file="test_wig_01_output_a.bw"/> 29 <output name="output" file="test_wig_01_output_a.bw"/>
35 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> 30 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
36 </test> 31 </test>
37 32 <test>
38 <test><!-- cached reference genome --> 33 <!-- cached reference genome -->
39 <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" /> 34 <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18"/>
40 <param name="index_source" value="cached"/> 35 <param name="index_source" value="cached"/>
41
42 <output name="output" file="test_wig_01_output_a.bw"/> 36 <output name="output" file="test_wig_01_output_a.bw"/>
43 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> 37 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
44 </test> 38 </test>
45 </tests> 39 </tests>
46 <help><![CDATA[ 40 <help><![CDATA[
55 similar to wiggle format and can be converted into BigWig format using UCSC 49 similar to wiggle format and can be converted into BigWig format using UCSC
56 wigToBigWig tool. We export files in bedGraph because it is usually much 50 wigToBigWig tool. We export files in bedGraph because it is usually much
57 smaller than file in wiggle format, and more importantly, CrossMap 51 smaller than file in wiggle format, and more importantly, CrossMap
58 internally transforms wiggle into bedGraph to increase running speed. 52 internally transforms wiggle into bedGraph to increase running speed.
59 ]]></help> 53 ]]></help>
60
61 <citations> 54 <citations>
62 <citation type="doi">10.1093/bioinformatics/btt730</citation> 55 <citation type="doi">10.1093/bioinformatics/btt730</citation>
63 </citations> 56 </citations>
64 </tool> 57 </tool>