# HG changeset patch
# User iuc
# Date 1718688992 0
# Node ID 3198f52bffaab29ec8cc95bb0d170dd051ab3186
# Parent  928a52b5c93839a07fcfb4585fffea61ba60a135
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3

diff -r 928a52b5c938 -r 3198f52bffaa brew3r.r_script.R
--- a/brew3r.r_script.R	Tue Jun 11 08:26:37 2024 +0000
+++ b/brew3r.r_script.R	Tue Jun 18 05:36:32 2024 +0000
@@ -91,17 +91,23 @@
         multi.strand.query <- ov.simple$queryHits[duplicated(ov.simple$queryHits)]
         to.remove <- unstranded.intervals[multi.strand.query]
         # Remove these potentially error-prone intervals from the template
-        input_gr_template <- input_gr_template[-to.remove]
+        if (length(to.remove) > 0) {
+            input_gr_template <- input_gr_template[-to.remove]
+        }
     }
 }
 
 # Run BREW3R.r main function
-new_gr_exons <- extend_granges(
-    input_gr_to_extend = input_gr_to_extend,
-    input_gr_to_overlap = input_gr_template,
-    add_new_exons = is.null(opt$no_add),
-    overlap_resolution_fn = opt$sup_output
-)
+if (length(input_gr_template) > 0) {
+    new_gr_exons <- extend_granges(
+        input_gr_to_extend = input_gr_to_extend,
+        input_gr_to_overlap = input_gr_template,
+        add_new_exons = is.null(opt$no_add),
+        overlap_resolution_fn = opt$sup_output
+    )
+} else {
+    new_gr_exons <- subset(input_gr_to_extend, type == "exon")
+}
 # Prevent extension using pattern
 if (!is.null(opt$exclude_pattern)) {
     input_gr_pattern <- subset(
diff -r 928a52b5c938 -r 3198f52bffaa brew3r_r.xml
--- a/brew3r_r.xml	Tue Jun 11 08:26:37 2024 +0000
+++ b/brew3r_r.xml	Tue Jun 18 05:36:32 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="brew3r_r" name="BREW3R.r" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
     <description>Extend GTF</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.0.1</token>
+        <token name="@TOOL_VERSION@">1.0.2</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <edam_topics>
@@ -114,6 +114,12 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="1">
+            <param name="gtf_to_extend" value="input2.gtf"/>
+            <param name="gtf_to_overlap" value="second_input2.gtf"/>
+            <param name="filter_unstranded" value="true"/>
+            <output name="output" value="output2.gtf" compare="diff" lines_diff="2"/>
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r 928a52b5c938 -r 3198f52bffaa test-data/input2.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2.gtf	Tue Jun 18 05:36:32 2024 +0000
@@ -0,0 +1,8 @@
+chr12	HAVANA	gene	11208360	11208972	.	-	.	gene_id "ENSMUSG00000047002.2"; gene_type "protein_coding"; gene_name "Msgn1"; level 2; mgi_id "MGI:1860483"; havana_gene "OTTMUSG00000065713.1";
+chr12	HAVANA	transcript	11208360	11208972	.	-	.	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
+chr12	HAVANA	exon	11208360	11208972	.	-	.	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; exon_number 1; exon_id "ENSMUSE00000372682.2"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
+chr12	HAVANA	CDS	11208385	11208948	.	-	0	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; exon_number 1; exon_id "ENSMUSE00000372682.2"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
+chr12	HAVANA	start_codon	11208946	11208948	.	-	0	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; exon_number 1; exon_id "ENSMUSE00000372682.2"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
+chr12	HAVANA	stop_codon	11208382	11208384	.	-	0	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; exon_number 1; exon_id "ENSMUSE00000372682.2"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
+chr12	HAVANA	UTR	11208360	11208384	.	-	.	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; exon_number 1; exon_id "ENSMUSE00000372682.2"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
+chr12	HAVANA	UTR	11208949	11208972	.	-	.	gene_id "ENSMUSG00000047002.2"; transcript_id "ENSMUST00000049877.2"; gene_type "protein_coding"; gene_name "Msgn1"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; exon_number 1; exon_id "ENSMUSE00000372682.2"; level 2; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; mgi_id "MGI:1860483"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_gene "OTTMUSG00000065713.1"; havana_transcript "OTTMUST00000159929.1";
diff -r 928a52b5c938 -r 3198f52bffaa test-data/output2.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output2.gtf	Tue Jun 18 05:36:32 2024 +0000
@@ -0,0 +1,5 @@
+##gff-version 2
+##source-version rtracklayer 1.64.0
+##date 2024-06-17
+chr12	HAVANA	exon	11206635	11208972	.	-	.	gene_id "ENSMUSG00000047002.2"; gene_type "protein_coding"; gene_name "Msgn1"; level "2"; mgi_id "MGI:1860483"; havana_gene "OTTMUSG00000065713.1"; transcript_id "ENSMUST00000049877.2"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_transcript "OTTMUST00000159929.1"; exon_number "1"; exon_id "ENSMUSE00000372682.2.ext"
+chr12	HAVANA	CDS	11208385	11208948	.	-	0	gene_id "ENSMUSG00000047002.2"; gene_type "protein_coding"; gene_name "Msgn1"; level "2"; mgi_id "MGI:1860483"; havana_gene "OTTMUSG00000065713.1"; transcript_id "ENSMUST00000049877.2"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_transcript "OTTMUST00000159929.1"; exon_number "1"; exon_id "ENSMUSE00000372682.2"
diff -r 928a52b5c938 -r 3198f52bffaa test-data/second_input2.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/second_input2.gtf	Tue Jun 18 05:36:32 2024 +0000
@@ -0,0 +1,4 @@
+# stringtie --merge -p 1 -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 0 -o /corral4/main/jobs/058/624/58624799/outputs/dataset_e626922f-3377-439f-bc63-2193dd017e36.dat /corral4/main/objects/a/e/8/dataset_ae875209-99bf-48a6-bd59-45c943915adc.dat /corral4/main/objects/f/f/5/dataset_ff53bd57-a0dd-43e1-b6b6-90dcfd194387.dat /corral4/main/objects/5/7/6/dataset_576d5eb0-adec-401b-8a75-de23a08db14a.dat
+# StringTie version 2.1.7
+chr12	StringTie	transcript	11206635	11209072	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 
+chr12	StringTie	exon	11206635	11209072	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1";