diff gff3_extract_sequence.xml @ 0:f678e282b320 draft default tip

"planemo upload"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_extract_sequence.xml	Fri May 06 07:07:23 2022 +0000
@@ -0,0 +1,71 @@
+<?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>