# HG changeset patch
# User iuc
# Date 1634832635 0
# Node ID be6bbdeafcb8ce3b6b2e9a5c5bbc01573b0bbbd2
# Parent  f91548912113489546746ca9a0c7dd701505b22d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 3309bdde7b03c5c250a020b0aee221133d9ea79b"

diff -r f91548912113 -r be6bbdeafcb8 metaeuk_easy_predict.xml
--- a/metaeuk_easy_predict.xml	Sun Jul 18 17:41:54 2021 +0000
+++ b/metaeuk_easy_predict.xml	Thu Oct 21 16:10:35 2021 +0000
@@ -1,7 +1,10 @@
 <tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0">
     <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description>
+    <xrefs>
+        <xref type="bio.tools">MetaEuk</xref>
+    </xrefs>
     <macros>
-        <token name="@TOOL_VERSION@">4.a0f584d</token>
+        <token name="@TOOL_VERSION@">5.34c21f2</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
@@ -22,7 +25,9 @@
             --max-intron '${adv.max_intron}'
             --min-intron '${adv.min_intron}'
         #end if
+        --write-frag-coords $write_frag_coords
         && mv output.fasta.codon.fas '$output'
+        && mv output.fasta.gff '$gff_output'
     ]]></command>
     <inputs>
         <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
@@ -43,9 +48,14 @@
             <when value="no">
             </when>
         </conditional>
+        <param name="write_frag_coords" type="select" value="0" label="Write the contig coords of the stop-to-stop fragment in which putative exon lies" help="The fragment coordinates in square brackets refer to the original fragment in which the exon was found." >
+            <option value="0">Yes</option>
+            <option value="1">No</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="fasta" />
+        <data name="gff_output" format="gff" />
     </outputs>
 
     <tests>
@@ -53,10 +63,12 @@
             <param name="contigs" ftype="fasta" value="contigs.fna" />
             <param name="query" ftype="fasta" value="proteins.faa" />
             <output name="output" ftype="fasta" value="output.fasta" />
+            <output name="gff_output" ftype="gff" value="output.gff" />
         </test>
         <test>
             <param name="contigs" ftype="fasta" value="contigs.fna" />
             <param name="query" ftype="fasta" value="proteins.faa" />
+            <param name="write_frag_coords" value="1" />
             <conditional name="adv">
                 <param name="adv_options" value="yes" />
                 <param name="max_intron" value="1000" />
@@ -64,7 +76,8 @@
             <assert_command>
                 <has_text text="--max-intron '1000'" />
             </assert_command>            
-            <output name="output" ftype="fasta" value="output.fasta" />
+            <output name="output" ftype="fasta" value="output_w_frag_coords.fasta" />
+            <output name="gff_output" ftype="gff" value="output.gff" />
         </test>
     </tests>
     <help><![CDATA[
diff -r f91548912113 -r be6bbdeafcb8 test-data/output.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.gff	Thu Oct 21 16:10:35 2021 +0000
@@ -0,0 +1,14 @@
+my_multi_exon_contig_1	gene	MetaEuk	101	1142	629	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+
+my_multi_exon_contig_1	mRNA	MetaEuk	101	1142	629	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA;Parent=identical_all_3_exons|my_multi_exon_contig_1|+
+my_multi_exon_contig_1	exon	MetaEuk	101	430	235	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_exon;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA
+my_multi_exon_contig_1	CDS	MetaEuk	101	430	235	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_CDS;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_exon
+my_multi_exon_contig_1	exon	MetaEuk	481	882	272	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_exon;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA
+my_multi_exon_contig_1	CDS	MetaEuk	481	882	272	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_CDS;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_exon
+my_multi_exon_contig_1	exon	MetaEuk	945	1142	128	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_exon;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA
+my_multi_exon_contig_1	CDS	MetaEuk	969	1142	128	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_CDS;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_exon
+my_multi_exon_contig_2	gene	MetaEuk	101	723	402	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+
+my_multi_exon_contig_2	mRNA	MetaEuk	101	723	402	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_mRNA;Parent=identical_all_2_exons|my_multi_exon_contig_2|+
+my_multi_exon_contig_2	exon	MetaEuk	101	430	235	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_exon;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_mRNA
+my_multi_exon_contig_2	CDS	MetaEuk	101	430	235	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_CDS;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_exon
+my_multi_exon_contig_2	exon	MetaEuk	481	723	166	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_exon;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_mRNA
+my_multi_exon_contig_2	CDS	MetaEuk	481	723	166	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_CDS;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_exon
diff -r f91548912113 -r be6bbdeafcb8 test-data/output_w_frag_coords.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_w_frag_coords.fasta	Thu Oct 21 16:10:35 2021 +0000
@@ -0,0 +1,4 @@
+>identical_all_3_exons|my_multi_exon_contig_1|+|629|7.362e-187|3|100|1141|[82]100[100]:[468]429[429]:330[330]|[477]480[480]:[884]881[881]:402[402]|[866]944[968]:[1147]1141[1141]:198[174]
+ATGACTTTATGCGCAGGTTTTGACCCTAATCGATTTTTGCCCATCGTTCTCGACGTTGGCACCAACAATGAAACCCATCGTAAAAATCATCAATACATGGGTTTAAGAAAGGACCGTGTTCACGGTGAGCAGTATGACATCTTTTTGGAGAACGTTATTAAAGCCATTCGTGAAGTCTTTCCCGAGGCCTTTATTCACTTTGAGGATTTCGGACTTAAAAATGCCAAAAGGATTTTAGACCACTATCGTCCTAATATTGCCTGTTTTAACGATGATATCCAGGGCACCGGTGCTGTAGCACTGGCCGCCATTATAGGCGCCCTTCATGTTACGAAGTCTCCCTTAACCGAGCAGCGCATCATGATCTTTGGTGCTGGTACTGCTGGTGTTGGTATCGCCAACCAAATTGTCGCTGGTATGGTGACAGATGGCCTTTCATTAGGTAAGGCTAGAGATAATCTTTTCATGATTGATCGATGCGGTTTGCTTCTGGAGAGACATGCTAAGATTGCTACTGATGGACAAAAGCCATTTTTGAAGAAGGACTCAGACTTTAAGGAAGTCCCTTCTGGAGACATTGATTTAGAGACTGCTATTTCACTAATCAAACCCACTGTTCTTCTGGGGTGCTCCGGTCAACCTGGAAAATTTACAGAAAAGGCCATTCGTGAAATGAGCAAGCATGTCAAACATCCCATCATCTTCCCAATCTCTAACCCCACCACTCTCATGAAGCCCGTTCAAATTGACGAATGGTCTAATGGTAAAGCTTTGATGGCAACTGGTTCTCCACTTCCTCCTCTCACACGTAATGGTAAAGAATATGTGATTTCTCAATGCAATAATGCTCTTCTTTACCCTGCTCTAGGTGTTGCATGTGTGTTATCCCGTTGCAAATTGTTGAGC
+>identical_all_2_exons|my_multi_exon_contig_2|+|402|1.588e-118|2|100|722|[82]100[100]:[468]429[429]:330[330]|[477]480[480]:[740]722[722]:243[243]
+ATGACTTTATGCGCAGGTTTTGACCCTAATCGATTTTTGCCCATCGTTCTCGACGTTGGCACCAACAATGAAACCCATCGTAAAAATCATCAATACATGGGTTTAAGAAAGGACCGTGTTCACGGTGAGCAGTATGACATCTTTTTGGAGAACGTTATTAAAGCCATTCGTGAAGTCTTTCCCGAGGCCTTTATTCACTTTGAGGATTTCGGACTTAAAAATGCCAAAAGGATTTTAGACCACTATCGTCCTAATATTGCCTGTTTTAACGATGATATCCAGGGCACCGGTGCTGTAGCACTGGCCGCCATTATAGGCGCCCTTCATGTTGATGGAATGCTGAAAGCAGCTTCCGATGCTTTGGCCACTGTTCCTAGATCTTTGTTTGTCGCCGATGAAGCTCTCTTGCCAGATCTGGACAATGCTCGAGAAATCTCTCGTCACATCGTTTTTGCGGTTTTGAAGCAAGCCATTTCTGAAGGAATGAGCACAGTGGATTTACCCAAAGATGATGCCAAGTTGAAGGAATGGATTATTGAACGAGAATGGAACCCTGAATACAGGAATTTTGTA