Mercurial > repos > bgruening > glimmer_glimmer_to_gff
comparison glimmer_glimmer_to_gff.xml @ 0:650106d2da39 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author | bgruening |
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date | Tue, 28 Nov 2017 10:09:27 -0500 |
parents | |
children | 891b330ffd94 |
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-1:000000000000 | 0:650106d2da39 |
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1 <tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@"> | |
2 <description></description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command><![CDATA[ | |
8 python '$__tool_directory__/glimmer_glimmer_to_gff.py' | |
9 '$input' > '$output' | |
10 ]]></command> | |
11 <inputs> | |
12 <param name="input" type="data" format="tabular" label="Glimmer Output File"/> | |
13 </inputs> | |
14 <outputs> | |
15 <data name="output" format="gff"/> | |
16 </outputs> | |
17 <tests> | |
18 <test> | |
19 <param name="input" value="glimmer_w_icm_trans-table-11_genomic.out" /> | |
20 <output name="output" file='glimmer.gff'/> | |
21 </test> | |
22 </tests> | |
23 <help><![CDATA[ | |
24 | |
25 **What it does** | |
26 | |
27 Converts a Glimmer3 output File to an GFF Annotation File:: | |
28 | |
29 **Example** | |
30 | |
31 Input:: | |
32 >contig00097 sbe.0.234 | |
33 orf00003 2869 497 -2 5.60 | |
34 orf00005 3894 2875 -1 7.05 | |
35 orf00007 4242 4826 +3 8.04 | |
36 orf00010 4846 5403 +1 8.57 | |
37 orf00012 6858 5413 -1 10.87 | |
38 orf00013 6857 7594 +2 3.61 | |
39 orf00014 7751 9232 +2 11.34 | |
40 orf00015 9374 10357 +2 10.66 | |
41 orf00017 10603 11196 +1 13.39 | |
42 orf00021 11303 11911 +2 8.81 | |
43 orf00025 14791 12050 -2 13.51 | |
44 orf00026 15216 16199 +3 6.37 | |
45 orf00028 16333 16935 +1 8.86 | |
46 | |
47 | |
48 Output: | |
49 contig00097 sbe.0.234 glimmer gene 497 2869 . - . -2 5.60 | |
50 contig00097 sbe.0.234 glimmer gene 2875 3894 . - . -1 7.05 | |
51 contig00097 sbe.0.234 glimmer gene 4242 4826 . + . +3 8.04 | |
52 contig00097 sbe.0.234 glimmer gene 4846 5403 . + . +1 8.57 | |
53 contig00097 sbe.0.234 glimmer gene 5413 6858 . - . -1 10.87 | |
54 contig00097 sbe.0.234 glimmer gene 6857 7594 . + . +2 3.61 | |
55 contig00097 sbe.0.234 glimmer gene 7751 9232 . + . +2 11.34 | |
56 contig00097 sbe.0.234 glimmer gene 9374 10357 . + . +2 10.66 | |
57 contig00097 sbe.0.234 glimmer gene 10603 11196 . + . +1 13.39 | |
58 contig00097 sbe.0.234 glimmer gene 11303 11911 . + . +2 8.81 | |
59 contig00097 sbe.0.234 glimmer gene 12050 14791 . - . -2 13.51 | |
60 contig00097 sbe.0.234 glimmer gene 15216 16199 . + . +3 6.37 | |
61 contig00097 sbe.0.234 glimmer gene 16333 16935 . + . +1 8.86 | |
62 | |
63 ]]></help> | |
64 <expand macro="citation" /> | |
65 </tool> |