Mercurial > repos > cpt > cpt_convert_glimmer

comparison cpt_convert_glimmer_to_gff3.xml @ 7:843ea2c82e9a draft

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author cpt
date Mon, 05 Jun 2023 02:40:30 +0000
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1 <tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0">
2 <description>convert formats</description>
3 <macros>
4 <import>cpt-macros.xml</import>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 @GENOME_SELECTOR_PRE@
10
11 'python $__tool_directory__/cpt_convert_glimmer_to_gff3.py'
12 '$glimmer'
13 @GENOME_SELECTOR@
14 > '$data' ]]>
15 </command>
16 <inputs>
17 <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
18 <expand macro="genome_selector"/>
19 </inputs>
20 <outputs>
21 <data format="gff3" name="data">
22 </data>
23 </outputs>
24 <tests>
25 <test>
26 <param name="reference_genome_source" value="history"/>
27 <param name="genome_fasta" value="ConvGlim_In.fasta"/>
28 <param name="glimmer" value="ConvGlim_In.out"/>
29 <output name="data" file="ConvGlim_Out.gff3"/>
30 </test>
31 </tests>
32 <help>
33 **What it does**
34
35 Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping
36 around over the sequence boundary (as if circular) then it will only convert the upstream fragment and
37 label it as "_truncated" in the resulting GFF.
38 </help>
39 <expand macro="citations"/>
40 </tool>