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comparison crossmap_gff.xml @ 4:e54eff8a4c3d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:08:05 -0400
parents abd0775e221f
children bb8290b7d207
comparison
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3:abd0775e221f 4:e54eff8a4c3d
1 <tool id="crossmap_gff" name="CrossMap GFF" version="@WRAPPER_VERSION@-0"> 1 <tool id="crossmap_gff" name="CrossMap GFF" version="@WRAPPER_VERSION@">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description> 2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
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 '${output}' 19 output
20 ]]></command> 20 ]]></command>
21 21
22 <inputs> 22 <inputs>
23 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/> 23 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
24 24
26 26
27 <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/> 27 <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
28 </inputs> 28 </inputs>
29 29
30 <outputs> 30 <outputs>
31 <data name="output" format="gff" label="${tool.name} on ${on_string}" /> 31 <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output" />
32 </outputs> 32 </outputs>
33 33
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> 36 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
72 72
73 - Each feature (exon, intron, UTR, etc) is processed separately and 73 - Each feature (exon, intron, UTR, etc) is processed separately and
74 independently, and we do NOT check if features originally belonging to 74 independently, and we do NOT check if features originally belonging to
75 the same gene were converted into the same gene. 75 the same gene were converted into the same gene.
76 - If user want to liftover gene annotation files, use BED12 format. 76 - If user want to liftover gene annotation files, use BED12 format.
77
78 ]]></help> 77 ]]></help>
79 78
80 <citations> 79 <citations>
81 <citation type="doi">10.1093/bioinformatics/btt730</citation> 80 <citation type="doi">10.1093/bioinformatics/btt730</citation>
82 </citations> 81 </citations>