Mercurial > repos > cpt_testbed > suite_work2
diff cpt_convert_glimmer_to_gff3.xml @ 0:d5c3354c166d draft default tip
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| author | cpt_testbed |
|---|---|
| date | Fri, 29 Apr 2022 10:33:36 +0000 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer_to_gff3.xml Fri Apr 29 10:33:36 2022 +0000 @@ -0,0 +1,41 @@ +<?xml version="1.0"?> +<tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0"> + <description>convert formats</description> + <macros> + <import>cpt-macros.xml</import> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"> +@GENOME_SELECTOR_PRE@ + +python $__tool_directory__/cpt_convert_glimmer_to_gff3.py +$glimmer +@GENOME_SELECTOR@ +> $data +</command> + <inputs> + <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/> + <expand macro="genome_selector" /> + </inputs> + <outputs> + <data format="gff3" name="data"> + </data> + </outputs> + <tests> + <test> + <param name="reference_genome_source" value="history" /> + <param name="genome_fasta" value="ConvGlim_In.fasta" /> + <param name="glimmer" value="ConvGlim_In.out" /> + <output name="data" file="ConvGlim_Out.gff3" /> + </test> + </tests> + <help> + **What it does** + + Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping + around over the sequence boundary (as if circular) then it will only convert the upstream fragment and + label it as "_truncated" in the resulting GFF. + </help> + <expand macro="citations" /> +</tool>