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comparison crossmap_gff.xml @ 2:aeecd2650942 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 12:39:42 -0400
parents de420379eb28
children abd0775e221f
comparison
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1:928c56d152cd 2:aeecd2650942
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 CrossMap.py gff 11 CrossMap.py gff
12 '${chain_source.input_chain}' 12 '${chain_source.input_chain}'
13 '${seq_source.input}' 13 '${input}'
14 14
15 #if str($include_fails) == "True" 15 #if str($include_fails) == "True"
16 > 16 >
17 #end if 17 #end if
18 18
19 '${output}' 19 '${output}'
20 ]]></command> 20 ]]></command>
21 21
22 <inputs> 22 <inputs>
23 <conditional name="seq_source"> 23 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
24 <expand macro="source" />
25 24
26 <when value="cached">
27 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
28 <validator type="unspecified_build"/>
29 <!-- Gives error in tests
30 <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."/>
31 -->
32 </param>
33 </when>
34 <when value="history">
35 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file"/>
36 </when>
37 </conditional>
38 <expand macro="chain" /> 25 <expand macro="chain" />
39 26
40 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/> 27 <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
41 </inputs> 28 </inputs>
42 29
43 <outputs> 30 <outputs>
44 <!-- GTF/GFF3? test... --> 31 <data name="output" format="gff" label="${tool.name} on ${on_string}" />
45 <data format="gff" name="output" label="${tool.name} on ${on_string}" />
46 </outputs> 32 </outputs>
47 33
48 <tests> 34 <tests>
49 <!-- GFF -->
50 <test> 35 <test>
51 <param name="input_format" value="gff"/> 36 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
52 <param name="index_source" value="history"/> 37 <param name="index_source" value="history"/>
53 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
54 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 38 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
55 <param name="include_fails" value="False"/> 39 <param name="include_fails" value="False"/>
56 40
57 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> 41 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
58 </test> 42 </test>
59 <test> 43 <test>
60 <param name="input_format" value="gff"/> 44 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
61 <param name="index_source" value="history"/> 45 <param name="index_source" value="history"/>
46 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
47 <param name="include_fails" value="True"/>
48
49 <output name="output" file="test_gff_01_output_a__all.gtf"/>
50 </test>
51 <test><!-- cached chain file -->
62 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> 52 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
63 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 53 <param name="index_source" value="cached"/>
64 <param name="include_fails" value="True"/> 54 <param name="include_fails" value="True"/>
65 55
66 <output name="output" file="test_gff_01_output_a__all.gtf"/> 56 <output name="output" file="test_gff_01_output_a__all.gtf"/>
67 </test> 57 </test>
68 </tests> 58 </tests>
71 61
72 GFF / GTF 62 GFF / GTF
73 --------- 63 ---------
74 Your input data should be either GTF/GFF2.5 or GFF3 format. 64 Your input data should be either GTF/GFF2.5 or GFF3 format.
75 65
76 GFF (General Feature Format) is another plain text file used to describe 66 GFF (General Feature Format) is another plain text file used to describe
77 gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The 67 gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
78 first eight fields are the same as GFF. Only chromosome and genome 68 first eight fields are the same as GFF. Only chromosome and genome
79 coordinates are updated. The format of output is determined from the input. 69 coordinates are updated. The format of output is determined from the input.
80 70
81 NOTE: 71 Notes:
82 72
83 - Each feature (exon, intron, UTR, etc) is processed separately and 73 - Each feature (exon, intron, UTR, etc) is processed separately and
84 independently, and we do NOT check if features originally belonging to 74 independently, and we do NOT check if features originally belonging to
85 the same gene were converted into the same gene. 75 the same gene were converted into the same gene.
86 - If user want to liftover gene annotation files, use BED12 format. 76 - If user want to liftover gene annotation files, use BED12 format.
87 77
88 Please see `the manual <http://crossmap.sourceforge.net/#convert-gff-gtf-format-files>`__ for more details 78 ]]></help>
89 ]]></help>
90 79
91 <citations> 80 <citations>
92 <citation type="doi">10.1093/bioinformatics/btt730</citation> 81 <citation type="doi">10.1093/bioinformatics/btt730</citation>
93 </citations> 82 </citations>
94 </tool> 83 </tool>