Mercurial > repos > cpt > cpt_export_seq_unique
diff gff3_extract_sequence2.xml @ 1:ac766d7dd641 draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author | cpt |
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date | Mon, 05 Jun 2023 02:41:21 +0000 |
parents | |
children | 5e8787e39d30 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_extract_sequence2.xml Mon Jun 05 02:41:21 2023 +0000 @@ -0,0 +1,36 @@ +<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>