Mercurial > repos > cpt_testbed > cpt_addparents
diff gff3_add_parents_to_cds.xml @ 0:b6ff405a3481 draft default tip
Uploaded
| author | cpt_testbed |
|---|---|
| date | Fri, 29 Apr 2022 11:21:36 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_add_parents_to_cds.xml Fri Apr 29 11:21:36 2022 +0000 @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool id="edu.tamu.cpt.gff3.cdsParents" name="GFF3 Add Gene to CDS" version="19.1.0.0"> + <description>is one step of fixing a gene model--adding parent gene features to CDSs</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +$__tool_directory__/gff3_add_parents_to_cds.py +@INPUT_GFF@ +> $output]]></command> + <inputs> + <expand macro="gff3_input" /> + </inputs> + <outputs> + <data format="gff3" name="output"/> + </outputs> + <tests> + <test> + <param name="gff3_data" value="T7_AddParentIn.gff3" /> + <output name="output"> + <assert_contents> + <has_line line="##gff-version 3"/> + <has_n_lines n="10105" /> + </assert_contents> + </output> + </test> + <test> + <param name="gff3_data" value="Miro_AddParentIn.gff3" /> + <output name="output"> + <assert_contents> + <has_line line="##gff-version 3"/> + <has_n_lines n="829" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool updates the gene model in a GFF3, useful when a nonstandard gene model +has been applied. It finds all CDS features, **strips their parent features**, +then applies a gene-mRNA-CDS model, compliant with the standard GFF3 format. + +Warning: Use this tool only when it is absolutely necessary to fix a gene model. + + ]]></help> + <expand macro="citations" /> +</tool>