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comparison crossmap_bigwig.xml @ 2:fd6459edbad9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
author iuc
date Thu, 19 Oct 2017 12:39:02 -0400
parents fb5401ff7ca2
children d3051afe9a38
comparison
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1:9b8ee2aedca4 2:fd6459edbad9
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 9
10 <command><![CDATA[ 10 <command><![CDATA[
11 #set $input_file = str($seq_source.input) 11 CrossMap.py bigwig
12 '${chain_source.input_chain}'
13 '${input}'
14 '${output}'
12 15
13 CrossMap.py bigwig 16 && mv '${output}.bw' '${output}'
14 '${chain_source.input_chain}'
15 '${input_file}'
16 '${output}'
17
18 && mv '${output}.bw' '${output}'
19
20 ]]></command> 17 ]]></command>
21 18
22 <inputs> 19 <inputs>
23 <conditional name="seq_source"> 20 <param name="input" type="data" format="bigwig" label="BigWig file"/>
24 <expand macro="source" /> 21
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" /> 22 <expand macro="chain" />
38 </inputs> 23 </inputs>
39 24
40 <outputs> 25 <outputs>
41 <data format="bigwig" name="output" label="${tool.name} on ${on_string}" /> 26 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" />
42 </outputs> 27 </outputs>
43 28
44 <tests> 29 <tests>
45 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
46 <test> 30 <test>
47 <param name="input_format" value="bigwig"/> 31 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
48 <param name="index_source" value="history"/> 32 <param name="index_source" value="history"/>
33 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
34
35 <output name="output" file="test_bigwig_01_output_a.bw"/>
36 </test>
37 <test><!-- cached chain file -->
49 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/> 38 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
50 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 39 <param name="index_source" value="cached"/>
51 <param name="include_fails" value="False"/>
52 40
53 <output name="output" file="test_bigwig_01_output_a.bw"/> 41 <output name="output" file="test_bigwig_01_output_a.bw"/>
54 </test> 42 </test>
55 </tests> 43 </tests>
56 <help><![CDATA[ 44 <help><![CDATA[
57 @HELP_GENERAL@ 45 @HELP_GENERAL@
58 46
59 BigWig 47 BigWig
60 ------ 48 ------
61 49
62 Input wiggle data can be in variableStep (for data with irregular 50 Input wiggle data can be in variableStep (for data with irregular
63 intervals) or fixedStep (for data with regular intervals). Regardless of 51 intervals) or fixedStep (for data with regular intervals). Regardless of
64 the input, the output will always in bedGraph format. bedGraph format is 52 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 53 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 54 wigToBigWig tool. We export files in bedGraph because it is usually much
67 smaller than file in wiggle format, and more importantly, CrossMap 55 smaller than file in wiggle format, and more importantly, CrossMap
68 internally transforms wiggle into bedGraph to increase running speed. 56 internally transforms wiggle into bedGraph to increase running speed.
69 57
70 Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details 58 ]]></help>
71 ]]></help>
72 59
73 <citations> 60 <citations>
74 <citation type="doi">10.1093/bioinformatics/btt730</citation> 61 <citation type="doi">10.1093/bioinformatics/btt730</citation>
75 </citations> 62 </citations>
76 </tool> 63 </tool>