Mercurial > repos > bgruening > glimmer_glimmer_to_gff
view glimmer_glimmer_to_gff.xml @ 2:891b330ffd94 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 274d1f6804bfd0362fdcd2383bfdb32ca8fd634e"
author | iuc |
---|---|
date | Sun, 20 Mar 2022 10:07:15 +0000 |
parents | 650106d2da39 |
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<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@+galaxy1"> <description></description> <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command><![CDATA[ python '$__tool_directory__/glimmer_glimmer_to_gff.py' '$input' > '$output' ]]></command> <inputs> <param name="input" type="data" format="txt" label="Glimmer Output File"/> </inputs> <outputs> <data name="output" format="gff"/> </outputs> <tests> <test> <param name="input" value="glimmer_w_icm_trans-table-11_genomic.out" /> <output name="output" file='glimmer.gff'/> </test> </tests> <help><![CDATA[ **What it does** Converts a Glimmer3 output File to an GFF Annotation File:: **Example** Input:: >contig00097 sbe.0.234 orf00003 2869 497 -2 5.60 orf00005 3894 2875 -1 7.05 orf00007 4242 4826 +3 8.04 orf00010 4846 5403 +1 8.57 orf00012 6858 5413 -1 10.87 orf00013 6857 7594 +2 3.61 orf00014 7751 9232 +2 11.34 orf00015 9374 10357 +2 10.66 orf00017 10603 11196 +1 13.39 orf00021 11303 11911 +2 8.81 orf00025 14791 12050 -2 13.51 orf00026 15216 16199 +3 6.37 orf00028 16333 16935 +1 8.86 Output: contig00097 sbe.0.234 glimmer gene 497 2869 . - . -2 5.60 contig00097 sbe.0.234 glimmer gene 2875 3894 . - . -1 7.05 contig00097 sbe.0.234 glimmer gene 4242 4826 . + . +3 8.04 contig00097 sbe.0.234 glimmer gene 4846 5403 . + . +1 8.57 contig00097 sbe.0.234 glimmer gene 5413 6858 . - . -1 10.87 contig00097 sbe.0.234 glimmer gene 6857 7594 . + . +2 3.61 contig00097 sbe.0.234 glimmer gene 7751 9232 . + . +2 11.34 contig00097 sbe.0.234 glimmer gene 9374 10357 . + . +2 10.66 contig00097 sbe.0.234 glimmer gene 10603 11196 . + . +1 13.39 contig00097 sbe.0.234 glimmer gene 11303 11911 . + . +2 8.81 contig00097 sbe.0.234 glimmer gene 12050 14791 . - . -2 13.51 contig00097 sbe.0.234 glimmer gene 15216 16199 . + . +3 6.37 contig00097 sbe.0.234 glimmer gene 16333 16935 . + . +1 8.86 ]]></help> <expand macro="citation" /> </tool>