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comparison crossmap_gff.xml @ 10:8dd8edcd3970 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 12:00:25 +0000
parents bb8290b7d207
children
comparison
equal deleted inserted replaced
9:1b0de2da29a0 10:8dd8edcd3970
4 <import>macros.xml</import> 4 <import>macros.xml</import>
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
10 <command><![CDATA[ 9 <command><![CDATA[
11 CrossMap.py gff 10 CrossMap gff
12 '${chain_source.input_chain}' 11 '${chain_source.input_chain}'
13 '${input}' 12 '${input}'
14 13
15 #if str($include_fails) == "True" 14 #if str($include_fails) == "True"
16 > 15 >
17 #end if 16 #end if
18 17
19 output 18 output
20 ]]></command> 19 ]]></command>
21
22 <inputs> 20 <inputs>
23 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/> 21 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
24 22 <expand macro="chain"/>
25 <expand macro="chain" />
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')"/> 23 <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> 24 </inputs>
29
30 <outputs> 25 <outputs>
31 <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output" /> 26 <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output"/>
32 </outputs> 27 </outputs>
33
34 <tests> 28 <tests>
35 <test> 29 <test>
36 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> 30 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
37 <param name="index_source" value="history"/> 31 <param name="index_source" value="history"/>
38 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 32 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
39 <param name="include_fails" value="False"/> 33 <param name="include_fails" value="False"/>
40
41 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> 34 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
42 </test> 35 </test>
43 <test> 36 <test>
44 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> 37 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
45 <param name="index_source" value="history"/> 38 <param name="index_source" value="history"/>
46 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 39 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
47 <param name="include_fails" value="True"/> 40 <param name="include_fails" value="True"/>
48
49 <output name="output" file="test_gff_01_output_a__all.gtf"/> 41 <output name="output" file="test_gff_01_output_a__all.gtf"/>
50 </test> 42 </test>
51 <test><!-- cached chain file --> 43 <test>
44 <!-- cached chain file -->
52 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf" dbkey="hg18"/> 45 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf" dbkey="hg18"/>
53 <param name="index_source" value="cached"/> 46 <param name="index_source" value="cached"/>
54 <param name="include_fails" value="True"/> 47 <param name="include_fails" value="True"/>
55
56 <output name="output" file="test_gff_01_output_a__all.gtf"/> 48 <output name="output" file="test_gff_01_output_a__all.gtf"/>
57 </test> 49 </test>
58 </tests> 50 </tests>
59 <help><![CDATA[ 51 <help><![CDATA[
60 @HELP_GENERAL@ 52 @HELP_GENERAL@
73 - Each feature (exon, intron, UTR, etc) is processed separately and 65 - Each feature (exon, intron, UTR, etc) is processed separately and
74 independently, and we do NOT check if features originally belonging to 66 independently, and we do NOT check if features originally belonging to
75 the same gene were converted into the same gene. 67 the same gene were converted into the same gene.
76 - If user want to liftover gene annotation files, use BED12 format. 68 - If user want to liftover gene annotation files, use BED12 format.
77 ]]></help> 69 ]]></help>
78
79 <citations> 70 <citations>
80 <citation type="doi">10.1093/bioinformatics/btt730</citation> 71 <citation type="doi">10.1093/bioinformatics/btt730</citation>
81 </citations> 72 </citations>
82 </tool> 73 </tool>