Mercurial > repos > cpt > cpt_export_seq_unique
diff cpt_export_seq_unique/gff3_extract_sequence2.xml @ 0:aaed5a0c774c draft
Uploaded
author | cpt |
---|---|
date | Fri, 01 Jul 2022 13:43:49 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_export_seq_unique/gff3_extract_sequence2.xml Fri Jul 01 13:43:49 2022 +0000 @@ -0,0 +1,37 @@ +<?xml version="1.0"?> +<tool id="edu.tamu.cpt.gff3.export_seq_unique" name="Feature Sequence Export Unique" version="1.2"> + <description>specially modified for sending CDSs to blast</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +@GENOME_SELECTOR_PRE@ + +$__tool_directory__/gff3_extract_sequence.py +@GENOME_SELECTOR@ + +@INPUT_GFF@ + +--feature_filter unique_cds +$nodesc +> $default +2> $gff3 +]]></command> + <inputs> + <expand macro="genome_selector" /> + <expand macro="gff3_input" /> + <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/> + </inputs> + <outputs> + <data format="fasta" hidden="false" name="default"/> + <data format="gff3" hidden="false" name="gff3"/> + </outputs> + <help><![CDATA[ +**What it does** + +Extract fasta sequences from a parent genome. + ]]></help> + <expand macro="citations" /> +</tool>