Mercurial > repos > iuc > crossmap_wig
comparison crossmap_wig.xml @ 1:81986a56b281 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author | iuc |
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date | Fri, 20 Oct 2017 02:49:58 -0400 |
parents | 0e6f675cea09 |
children | d0e7cc22351f |
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0:0e6f675cea09 | 1:81986a56b281 |
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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 | |
11 '${chain_source.input_chain}' | |
12 '${input}' | |
13 '${output}' | |
10 | 14 |
11 #set $input_file = str($seq_source.input) | 15 && mv '${output}.bw' '${output}' |
12 | 16 && mv '${output}.sorted.bgr' '${output2}' |
13 CrossMap.py wig | |
14 '${chain_source.input_chain}' | |
15 '${input_file}' | |
16 '${output}' | |
17 | |
18 && mv '${output}.bw' '${output}' | |
19 && mv '${output}.sorted.bgr' '${output2}' | |
20 ]]></command> | 17 ]]></command> |
21 | 18 |
22 <inputs> | 19 <inputs> |
23 <conditional name="seq_source"> | 20 <param name="input" type="data" format="wig" label="Wiggle file"/> |
24 <expand macro="source" /> | 21 |
25 <when value="cached"> | |
26 <param format="wig" name="input" type="data" label="Wiggle file"> | |
27 <validator type="unspecified_build"/> | |
28 <!-- Gives error in tests | |
29 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/> | |
30 --> | |
31 </param> | |
32 </when> | |
33 <when value="history"> | |
34 <param format="wig" name="input" type="data" label="Wiggle file"/> | |
35 </when> | |
36 </conditional> | |
37 <expand macro="chain" /> | 22 <expand macro="chain" /> |
38 </inputs> | 23 </inputs> |
39 | 24 |
40 <outputs> | 25 <outputs> |
41 <data format="wig" name="output" label="${tool.name} on ${on_string}" /> | 26 <data name="output" format="wig" label="${tool.name} on ${on_string}" /> |
42 <data format="wig" name="output2" label="${tool.name} (bedgraph) on ${on_string}" /> | 27 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" /> |
43 </outputs> | 28 </outputs> |
44 | 29 |
45 <tests> | 30 <tests> |
46 <!-- WIG - Doesn't understand fixedStep --> | 31 <!-- WIG - Doesn't understand fixedStep --> |
47 <test> | 32 <test> |
33 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> | |
48 <param name="index_source" value="history"/> | 34 <param name="index_source" value="history"/> |
35 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> | |
36 | |
37 <output name="output" file="test_wig_01_output_a.bw"/> | |
38 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> | |
39 </test> | |
40 | |
41 <test> | |
49 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> | 42 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> |
50 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> | 43 <param name="index_source" value="cached"/> |
51 | 44 |
52 <output name="output" file="test_wig_01_output_a.bw"/> | 45 <output name="output" file="test_wig_01_output_a.bw"/> |
53 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> | 46 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> |
54 </test> | 47 </test> |
55 </tests> | 48 </tests> |
57 @HELP_GENERAL@ | 50 @HELP_GENERAL@ |
58 | 51 |
59 Wig | 52 Wig |
60 --- | 53 --- |
61 | 54 |
62 Input wiggle data can be in variableStep (for data with irregular | 55 Input wiggle data can be in variableStep (for data with irregular |
63 intervals) or fixedStep (for data with regular intervals). Regardless of | 56 intervals) or fixedStep (for data with regular intervals). Regardless of |
64 the input, the output will always in bedGraph format. bedGraph format is | 57 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 | 58 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 | 59 wigToBigWig tool. We export files in bedGraph because it is usually much |
67 smaller than file in wiggle format, and more importantly, CrossMap | 60 smaller than file in wiggle format, and more importantly, CrossMap |
68 internally transforms wiggle into bedGraph to increase running speed. | 61 internally transforms wiggle into bedGraph to increase running speed. |
69 | 62 |
70 Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details | 63 ]]></help> |
71 ]]></help> | |
72 | 64 |
73 <citations> | 65 <citations> |
74 <citation type="doi">10.1093/bioinformatics/btt730</citation> | 66 <citation type="doi">10.1093/bioinformatics/btt730</citation> |
75 </citations> | 67 </citations> |
76 </tool> | 68 </tool> |