# HG changeset patch
# User iuc
# Date 1573514866 18000
# Node ID 4dea028863377a9999b0b15f4e204bda30993c44
# Parent  6ea09f60dee99b569755a74511cf4cba9b3bb357
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432"

diff -r 6ea09f60dee9 -r 4dea02886337 gffread.xml
--- a/gffread.xml	Fri Nov 01 12:54:52 2019 -0400
+++ b/gffread.xml	Mon Nov 11 18:27:46 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="gffread" name="gffread" version="@VERSION@.1">
+<tool id="gffread" name="gffread" version="@VERSION@.0">
     <description>Filters and/or converts GFF3/GTF2 records</description>
     <macros>
-        <token name="@VERSION@">0.11.4</token>
+        <token name="@VERSION@">0.11.6</token>
         <xml name="fasta_output_select">
             <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
                 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
@@ -126,9 +126,7 @@
             <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
             <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
             <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
-            <!-- The no-pseudo option is broken in 0.11.4 of gffread.
-                 See https://github.com/gpertea/gffread/issues/43 -->
-            <!-- <option value="\-\-no-pseudo">filter out records matching the 'pseudo' keyword (\-\-no-pseudo)</option> -->
+            <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
         </param>
         <conditional name="region">
             <param name="region_filter" type="select" label="Filter by genome region">
@@ -269,20 +267,15 @@
             <param name="gff_fmt" value="gff"/>
             <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
         </test>
-
         <test>
             <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
             <param name="gff_fmt" value="gff"/>
             <param name="full_gff_attribute_preservation" value="-F"/>
             <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
         </test>
-        
-<!-- The no-pseudo option is broken in 0.11.4 of gffread.
-     See https://github.com/gpertea/gffread/issues/43 -->
-<!-- 
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
-            <param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting
+            <param name="filtering" value="--no-pseudo"/>
             <param name="gff_fmt" value="gtf"/>
             <output name="output_gtf">
                 <assert_contents>
@@ -290,8 +283,6 @@
                 </assert_contents>
             </output>
         </test>
--->
-
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="region_filter" value="filter"/>
@@ -304,7 +295,6 @@
                 </assert_contents>
             </output>
         </test>
-
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="region_filter" value="filter"/>
@@ -318,7 +308,6 @@
                 </assert_contents>
             </output>
         </test>
-
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="filtering" value="-C"/>
@@ -332,7 +321,6 @@
                 </assert_contents>
             </output>
         </test>
-
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="source" value="history"/>
diff -r 6ea09f60dee9 -r 4dea02886337 test-data/Homo_sapiens.GRCh37_19.71.gff3
--- a/test-data/Homo_sapiens.GRCh37_19.71.gff3	Fri Nov 01 12:54:52 2019 -0400
+++ b/test-data/Homo_sapiens.GRCh37_19.71.gff3	Mon Nov 11 18:27:46 2019 -0500
@@ -1,5 +1,5 @@
 # gffread /tmp/tmpq6d_yfqc/files/9/2/2/dataset_922cd54b-d77c-48fb-abf7-6fc8d8fdb97c.dat -o output.gff3
-# gffread v0.11.4
+# gffread v0.11.6
 ##gff-version 3
 19	snRNA	transcript	223158	223261	.	-	.	ID=ENST00000410397;geneID=ENSG00000222329;gene_name=U6
 19	snRNA	exon	223158	223261	.	-	.	Parent=ENST00000410397
diff -r 6ea09f60dee9 -r 4dea02886337 test-data/ecoli-k12.processed.gff3
--- a/test-data/ecoli-k12.processed.gff3	Fri Nov 01 12:54:52 2019 -0400
+++ b/test-data/ecoli-k12.processed.gff3	Mon Nov 11 18:27:46 2019 -0500
@@ -1,5 +1,5 @@
 # gffread /tmp/tmpq6d_yfqc/files/2/7/7/dataset_277f6e18-b25a-4b59-b712-49b5c202a183.dat -F -o output.gff3
-# gffread v0.11.4
+# gffread v0.11.6
 ##gff-version 3
 NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene-b0001;geneID=gene-b0001;gene_name=thrL;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001
 NC_000913.3	RefSeq	CDS	190	255	.	+	0	Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11