view gff3_extract_sequence.xml @ 0:f678e282b320 draft default tip

"planemo upload"

<?xml version="1.0"?>
<tool id="edu.tamu.cpt.gff3.export_seq" name="GFF3 Feature Sequence Export" version="19.1.0.0">
  <description>Export corresponding sequence in genome from GFF3</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@

#if $feature_filter and $feature_filter is not None:
--feature_filter $feature_filter
#end if
$nodesc
> $default]]></command>
  <inputs>
    <expand macro="genome_selector" />
    <expand macro="gff3_input" />
	<param label="Filter for specific feature types" name="feature_filter" type="text"
		help="Use 'nice_cds' if your features are coming from Apollo, however this will fail on non-Apollo data"/>
    <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/>
  </inputs>
  <outputs>
    <data format="fasta" hidden="false" name="default"/>
  </outputs>
  <tests>
		<test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="T7_ExtSeqIn.fasta" />
			<param name="gff3_data" value="T7_ExtSeqIn.gff3" />
			<param name="nodesc" value="" />
			<param name="feature_filter" value="CDS" />
			<output name="output" file="T7_ExtSeqOut.fasta" />
		</test>
                <test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="Miro_ExtSeqIn.fa" />
			<param name="gff3_data" value="Miro_ExtSeqIn.gff3" />
			<param name="nodesc" value="" />
			<param name="feature_filter" value="CDS" />
			<output name="output" file="Miro_ExtSeqOut1.fa" />
		</test>
		<test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="Miro_ExtSeqIn.fa" />
			<param name="gff3_data" value="Miro_ExtSeqIn.gff3" />
			<param name="feature_filter" value="CDS" />
			<param name="nodesc" value="--nodesc" />
			<output name="output" file="Miro_ExtSeqOut2.fa" />
		</test>
  </tests>
  <help><![CDATA[
**What it does**

From the FASTA sequence for a genome, extracts the *nucleotide* sequences for 
all CDSs in an input GFF3 and outputs them as a multi-FASTA formatted file.

The filter for specific feature types was designed for data retrieved from Apollo. 
Using ‘unique_cds’ extracts the sequence for all CDS. Using ‘nice_cds’ will extract 
the sequence only for CDS features with a start codon (recommended). If a gene from
Apollo has multiple CDSs, the tool will append a "_##" to the end of subsequent genes.

      ]]></help>
		<expand macro="citations" />
</tool>