# HG changeset patch
# User iuc
# Date 1728032254 0
# Node ID 860f8836c9364011971b6421fa31661f3214dc3d
# Parent  be6bbdeafcb8ce3b6b2e9a5c5bbc01573b0bbbd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 412a084cda6aeca8dfe0b0dbfff9c3426aec7707

diff -r be6bbdeafcb8 -r 860f8836c936 metaeuk_easy_predict.xml
--- a/metaeuk_easy_predict.xml	Thu Oct 21 16:10:35 2021 +0000
+++ b/metaeuk_easy_predict.xml	Fri Oct 04 08:57:34 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0">
+<tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy1" profile="23.0">
     <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description>
+    <macros>
+        <token name="@TOOL_VERSION@">7.bba0d80</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">MetaEuk</xref>
     </xrefs>
-    <macros>
-        <token name="@TOOL_VERSION@">5.34c21f2</token>
-    </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
     </requirements>
@@ -16,7 +16,7 @@
             '$query'
             output.fasta
             "./tmp/metaeuk_working"
-            --threads \${GALAXY_SLOTS:-1}
+            --threads "\${GALAXY_SLOTS:-1}"
             --min-length '${min_length}'
             -e '${segment_eval}'
             --metaeuk-eval '${metaeuk_eval}'
@@ -33,17 +33,17 @@
         <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
         <param name="query" type="data" format="fasta" label="Proteins to search against contigs" />
         <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" />
-        <param argument="--min-length" name="min_length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" />
-        <param argument="--metaeuk-eval" name="metaeuk_eval" type="float" value="0.001" label="Maximum e-value of combined exon set" />
-        <param argument="--metaeuk-tcov" name="metaeuk_tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" />
+        <param argument="--min-length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" />
+        <param argument="--metaeuk-eval" type="float" value="0.001" label="Maximum e-value of combined exon set" />
+        <param argument="--metaeuk-tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" />
         <conditional name="adv">
             <param type="select"  name="adv_options" label="Show advanced options">
                 <option value="yes">Yes</option>
                 <option value="no" selected="true">No</option>
             </param>
             <when value="yes">
-                <param argument="--max-intron" name="max_intron" value="10000" type="integer" label="Maximum intron size" />
-                <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" />
+                <param argument="--max-intron" value="10000" type="integer" label="Maximum intron size" />
+                <param argument="--min-intron" value="15" type="integer" label="Minimum intron size" />
             </when>
             <when value="no">
             </when>
@@ -54,8 +54,8 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output" format="fasta" />
-        <data name="gff_output" format="gff" />
+        <data name="output" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
+        <data name="gff_output" format="gff" label="${tool.name} on ${on_string}: GFF" />
     </outputs>
 
     <tests>
diff -r be6bbdeafcb8 -r 860f8836c936 test-data/output.gff
--- a/test-data/output.gff	Thu Oct 21 16:10:35 2021 +0000
+++ b/test-data/output.gff	Fri Oct 04 08:57:34 2024 +0000
@@ -1,14 +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
+my_multi_exon_contig_1	MetaEuk	gene	101	1142	629	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100
+my_multi_exon_contig_1	MetaEuk	mRNA	101	1142	629	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100
+my_multi_exon_contig_1	MetaEuk	exon	101	430	235	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_0;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA
+my_multi_exon_contig_1	MetaEuk	CDS	101	430	235	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_CDS_0;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_0
+my_multi_exon_contig_1	MetaEuk	exon	481	882	272	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_1;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA
+my_multi_exon_contig_1	MetaEuk	CDS	481	882	272	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_CDS_1;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_1
+my_multi_exon_contig_1	MetaEuk	exon	945	1142	128	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_2;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA
+my_multi_exon_contig_1	MetaEuk	CDS	969	1142	128	+	.	Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_CDS_2;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_2
+my_multi_exon_contig_2	MetaEuk	gene	101	723	402	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100
+my_multi_exon_contig_2	MetaEuk	mRNA	101	723	402	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_mRNA;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100
+my_multi_exon_contig_2	MetaEuk	exon	101	430	235	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_0;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_mRNA
+my_multi_exon_contig_2	MetaEuk	CDS	101	430	235	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_CDS_0;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_0
+my_multi_exon_contig_2	MetaEuk	exon	481	723	166	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_1;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_mRNA
+my_multi_exon_contig_2	MetaEuk	CDS	481	723	166	+	.	Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_CDS_1;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_1