# HG changeset patch
# User iuc
# Date 1702669164 0
# Node ID 3e436657dcd010017bcefc779a034b47a98c8674
# Parent  154d00cbbf2d8ba5e804836a2da369977b4d817d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac

diff -r 154d00cbbf2d -r 3e436657dcd0 gffread.xml
--- a/gffread.xml	Sat Sep 25 15:38:31 2021 +0000
+++ b/gffread.xml	Fri Dec 15 19:39:24 2023 +0000
@@ -1,12 +1,9 @@
 <tool id="gffread" name="gffread" version="@GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>Filters and/or converts GFF3/GTF2 records</description>
-    <xrefs>
-        <xref type="bio.tools">gffread</xref>
-    </xrefs>
     <macros>
         <!-- the version of this tool must not be lowered since in the past 2.x was used
             lets use small increments and hope that gffread catches up one day -->
-        <token name="@GALAXY_TOOL_VERSION@">2.2.1.3</token>
+        <token name="@GALAXY_TOOL_VERSION@">2.2.1.4</token>
         <token name="@TOOL_VERSION@">0.12.7</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <xml name="fasta_output_select">
@@ -55,6 +52,9 @@
             </param>
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">gffread</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">gffread</requirement>
     </requirements>
@@ -116,13 +116,13 @@
             #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
         #end if
     #end if
+
     #if $gffs.gff_fmt != 'none':
         #if $gffs.gff_fmt != 'bed' and $gffs.tname:
             -t '$gffs.tname'
         #end if
         #if $gffs.gff_fmt == 'gff':
-            ## TODO bug 'gft' -> 'gtf'
-            #if $input.datatype.file_ext == 'gft':
+            #if $input.datatype.file_ext == 'gtf':
                 $gffs.ensembl
             #end if
         #end if
@@ -132,6 +132,8 @@
             --bed
         #end if
         -o output.$gffs.gff_fmt
+    #else if 'fa_outputs' not in $reference_genome or '.fa' not in str($reference_genome['fa_outputs'])
+        -o output.gff
     #end if
 
 ## Missing options
@@ -253,11 +255,10 @@
         <conditional name="reference_genome">
             <param name="source" type="select" label="Reference Genome" help="NOTE: Required for fasta outputs">
                 <option value="none">none</option>
-                <option value="cached"></option>
+                <option value="cached">Cached reference data</option>
                 <option value="history">From your history</option>
             </param>
-            <when value="none">
-            </when>
+            <when value="none"/>
             <when value="cached">
                 <param argument="-g" name="fasta_indexes" type="select" label="Source FASTA Sequence">
                     <options from_data_table="all_fasta"/>
@@ -280,8 +281,7 @@
                 <option value="gtf">GTF</option>
                 <option value="bed">BED</option>
             </param>
-            <when value="none">
-            </when>
+            <when value="none"/>
             <when value="gff">
                 <param argument="-L" name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help=""/>
                 <expand macro="trackname" />
@@ -289,8 +289,7 @@
             <when value="gtf">
                 <expand macro="trackname" />
             </when>
-            <when value="bed">
-            </when>
+            <when value="bed"/>
         </conditional>
 
         <param argument="-F" name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
@@ -303,7 +302,8 @@
     </inputs>
     <outputs>
         <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff">
-            <filter>gffs['gff_fmt'] == 'gff'</filter>
+            <!-- output gff also if the user deselected all outputs: none is selected and all .fa outputs are disabled  -->
+            <filter>gffs['gff_fmt'] == 'gff' or (gffs['gff_fmt'] == 'none' and ('fa_outputs' not in reference_genome or '.fa' not in str(reference_genome['fa_outputs'])))</filter>
         </data>
         <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
             <filter>gffs['gff_fmt'] == 'gtf'</filter>
@@ -329,17 +329,67 @@
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="gff_fmt" value="gff"/>
             <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
+        </test>
+        <!-- mapping -->
+        <test expect_num_outputs="1">
+            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
+            <param name="gff_fmt" value="gff"/>
+            <param name="chr_replace" ftype="tabular" value="chr_replace"/>
+            <output name="output_gff" ftype="gff3">
+                <assert_contents>
+                    <has_n_lines n="314"/>
+                    <has_line_matching expression="^chr.*"/>
+                    <has_line_matching expression="^1.*" negate="true"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
+        </test>
+        <!-- none output and all .fa outputs deselected .. gff is produced anyway, since we need one output -->
+        <test expect_num_outputs="1">
+            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
+            <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
+        </test>
+        <!-- test ensemble gtf to gff conversion -->
+        <test expect_num_outputs="1">
+            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
+            <conditional name="gffs">
+                <param name="gff_fmt" value="gff"/>
+                <param name="ensembl" value="true"/>
+                <param name="tname" value="track name"/>
+            </conditional>
+            <output name="output_gff" file="Homo_sapiens.GRCh37_19.71_ensemble.gff3" ftype="gff3" lines_diff="4" />
+            <assert_command>
+                <has_text text="-L"/>
+                <has_text text="-t &#39;track name&#39;"/>
+            </assert_command>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="gff_fmt" value="gff"/>
             <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <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="4" />
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <!-- bed output -->
         <test expect_num_outputs="1">
@@ -351,6 +401,9 @@
                     <has_n_columns n="13"/>
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <!-- bed input and test tname -->
         <test expect_num_outputs="1">
@@ -365,6 +418,9 @@
                     <has_text text="track name"/>
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
@@ -377,6 +433,9 @@
                     <has_text text="ENST00000382683" />
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
@@ -390,6 +449,9 @@
                     <has_text text="ENST00000382683" />
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
@@ -403,6 +465,9 @@
                     <has_text text="ENST00000382683" />
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="4">
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
@@ -436,6 +501,9 @@
                     <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <param name="input" ftype="gtf" value="stop_codons.gtf"/>
@@ -448,6 +516,9 @@
                     <has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" />
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_n_lines n="0"/>
+            </assert_stdout>
         </test>
     </tests>
     <help>
diff -r 154d00cbbf2d -r 3e436657dcd0 test-data/Homo_sapiens.GRCh37_19.71_ensemble.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Homo_sapiens.GRCh37_19.71_ensemble.gff3	Fri Dec 15 19:39:24 2023 +0000
@@ -0,0 +1,314 @@
+##gff-version 3
+# gffread v0.12.7
+# gffread /tmp/tmpvxc_8nmx/files/9/a/6/dataset_9a6a5831-b7ee-4eee-9b23-08af98672088.dat -L -o /home/berntm/projects/tools-iuc/tools/gffread/test-data/Homo_sapiens.GRCh37_19.71_ensemble.gff3 -t track name
+19	track name	transcript	223158	223261	.	-	.	ID=ENST00000410397;geneID=ENSG00000222329;gene_name=U6;gene_biotype=snRNA;transcript_name=U6.795-201
+19	track name	exon	223158	223261	.	-	.	Parent=ENST00000410397
+19	track name	transcript	229640	230165	.	-	.	ID=ENST00000587910;geneID=ENSG00000267600;gene_name=AC098474.1;gene_biotype=pseudogene;transcript_name=AC098474.1-001
+19	track name	exon	229640	229709	.	-	.	Parent=ENST00000587910
+19	track name	exon	230084	230165	.	-	.	Parent=ENST00000587910
+19	track name	transcript	239145	239247	.	-	.	ID=ENST00000588755;geneID=ENSG00000267305;gene_name=CTD-3113P16.7;gene_biotype=pseudogene;transcript_name=CTD-3113P16.7-001
+19	track name	exon	239145	239247	.	-	.	Parent=ENST00000588755
+19	track name	transcript	279495	280170	.	+	.	ID=ENST00000589981;geneID=ENSG00000267447;gene_name=VN2R11P;gene_biotype=pseudogene;transcript_name=VN2R11P-001
+19	track name	exon	279495	280170	.	+	.	Parent=ENST00000589981
+19	track name	transcript	281043	291386	.	-	.	ID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-001;protein_id=ENSP00000269812
+19	track name	exon	281043	281537	.	-	.	Parent=ENST00000269812
+19	track name	exon	282134	282310	.	-	.	Parent=ENST00000269812
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000269812
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000269812
+19	track name	exon	288020	288171	.	-	.	Parent=ENST00000269812
+19	track name	exon	291285	291386	.	-	.	Parent=ENST00000269812
+19	track name	CDS	281388	281537	.	-	0	Parent=ENST00000269812
+19	track name	CDS	282134	282310	.	-	0	Parent=ENST00000269812
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000269812
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000269812
+19	track name	CDS	288020	288171	.	-	2	Parent=ENST00000269812
+19	track name	CDS	291285	291336	.	-	0	Parent=ENST00000269812
+19	track name	transcript	281345	291393	.	-	.	ID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-003;protein_id=ENSP00000388565
+19	track name	exon	281345	281537	.	-	.	Parent=ENST00000434325
+19	track name	exon	282134	282310	.	-	.	Parent=ENST00000434325
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000434325
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000434325
+19	track name	exon	288020	288171	.	-	.	Parent=ENST00000434325
+19	track name	exon	291326	291393	.	-	.	Parent=ENST00000434325
+19	track name	CDS	281388	281537	.	-	0	Parent=ENST00000434325
+19	track name	CDS	282134	282310	.	-	0	Parent=ENST00000434325
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000434325
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000434325
+19	track name	CDS	288020	288055	.	-	0	Parent=ENST00000434325
+19	track name	transcript	281388	291200	.	-	.	ID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-004;protein_id=ENSP00000329697
+19	track name	exon	281388	281537	.	-	.	Parent=ENST00000327790
+19	track name	exon	282134	282310	.	-	.	Parent=ENST00000327790
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000327790
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000327790
+19	track name	exon	288020	288171	.	-	.	Parent=ENST00000327790
+19	track name	exon	290952	291200	.	-	.	Parent=ENST00000327790
+19	track name	CDS	281388	281537	.	-	0	Parent=ENST00000327790
+19	track name	CDS	282134	282310	.	-	0	Parent=ENST00000327790
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000327790
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000327790
+19	track name	CDS	288020	288171	.	-	2	Parent=ENST00000327790
+19	track name	CDS	290952	291066	.	-	0	Parent=ENST00000327790
+19	track name	transcript	281991	287636	.	-	.	ID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-007;protein_id=ENSP00000466947
+19	track name	exon	281991	282310	.	-	.	Parent=ENST00000586998
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000586998
+19	track name	exon	287474	287636	.	-	.	Parent=ENST00000586998
+19	track name	CDS	282122	282310	.	-	0	Parent=ENST00000586998
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000586998
+19	track name	CDS	287474	287636	.	-	2	Parent=ENST00000586998
+19	track name	transcript	287161	288530	.	-	.	ID=ENST00000589672;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-006
+19	track name	exon	287161	287751	.	-	.	Parent=ENST00000589672
+19	track name	exon	288020	288530	.	-	.	Parent=ENST00000589672
+19	track name	transcript	287474	291382	.	-	.	ID=ENST00000591572;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-005;protein_id=ENSP00000466545
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000591572
+19	track name	exon	288020	288189	.	-	.	Parent=ENST00000591572
+19	track name	exon	291285	291382	.	-	.	Parent=ENST00000591572
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000591572
+19	track name	CDS	288020	288189	.	-	2	Parent=ENST00000591572
+19	track name	CDS	291285	291336	.	-	0	Parent=ENST00000591572
+19	track name	transcript	305573	306467	.	+	.	ID=ENST00000591533;geneID=ENSG00000267124;gene_name=CTD-3113P16.5;gene_biotype=antisense;transcript_name=CTD-3113P16.5-002
+19	track name	exon	305573	305703	.	+	.	Parent=ENST00000591533
+19	track name	exon	306057	306467	.	+	.	Parent=ENST00000591533
+19	track name	transcript	305575	344793	.	-	.	ID=ENST00000264819;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-001;protein_id=ENSP00000264819
+19	track name	exon	305575	306711	.	-	.	Parent=ENST00000264819
+19	track name	exon	307119	307536	.	-	.	Parent=ENST00000264819
+19	track name	exon	308577	308665	.	-	.	Parent=ENST00000264819
+19	track name	exon	308801	308925	.	-	.	Parent=ENST00000264819
+19	track name	exon	311845	311939	.	-	.	Parent=ENST00000264819
+19	track name	exon	312191	312272	.	-	.	Parent=ENST00000264819
+19	track name	exon	313492	313643	.	-	.	Parent=ENST00000264819
+19	track name	exon	325635	325704	.	-	.	Parent=ENST00000264819
+19	track name	exon	326507	326598	.	-	.	Parent=ENST00000264819
+19	track name	exon	327133	327256	.	-	.	Parent=ENST00000264819
+19	track name	exon	327864	327989	.	-	.	Parent=ENST00000264819
+19	track name	exon	334400	334542	.	-	.	Parent=ENST00000264819
+19	track name	exon	336083	336173	.	-	.	Parent=ENST00000264819
+19	track name	exon	344774	344793	.	-	.	Parent=ENST00000264819
+19	track name	CDS	306690	306711	.	-	1	Parent=ENST00000264819
+19	track name	CDS	307119	307536	.	-	2	Parent=ENST00000264819
+19	track name	CDS	308577	308665	.	-	1	Parent=ENST00000264819
+19	track name	CDS	308801	308925	.	-	0	Parent=ENST00000264819
+19	track name	CDS	311845	311939	.	-	2	Parent=ENST00000264819
+19	track name	CDS	312191	312272	.	-	0	Parent=ENST00000264819
+19	track name	CDS	313492	313643	.	-	2	Parent=ENST00000264819
+19	track name	CDS	325635	325704	.	-	0	Parent=ENST00000264819
+19	track name	CDS	326507	326598	.	-	2	Parent=ENST00000264819
+19	track name	CDS	327133	327256	.	-	0	Parent=ENST00000264819
+19	track name	CDS	327864	327989	.	-	0	Parent=ENST00000264819
+19	track name	CDS	334400	334542	.	-	2	Parent=ENST00000264819
+19	track name	CDS	336083	336173	.	-	0	Parent=ENST00000264819
+19	track name	CDS	344774	344782	.	-	0	Parent=ENST00000264819
+19	track name	transcript	305579	325706	.	+	.	ID=ENST00000589092;geneID=ENSG00000267124;gene_name=CTD-3113P16.5;gene_biotype=antisense;transcript_name=CTD-3113P16.5-001
+19	track name	exon	305579	305934	.	+	.	Parent=ENST00000589092
+19	track name	exon	325624	325706	.	+	.	Parent=ENST00000589092
+19	track name	transcript	326607	336178	.	-	.	ID=ENST00000586994;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-004
+19	track name	exon	326607	327256	.	-	.	Parent=ENST00000586994
+19	track name	exon	327864	327989	.	-	.	Parent=ENST00000586994
+19	track name	exon	334400	334542	.	-	.	Parent=ENST00000586994
+19	track name	exon	336083	336178	.	-	.	Parent=ENST00000586994
+19	track name	transcript	327864	340599	.	-	.	ID=ENST00000592722;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-003
+19	track name	exon	327864	327989	.	-	.	Parent=ENST00000592722
+19	track name	exon	330264	330380	.	-	.	Parent=ENST00000592722
+19	track name	exon	334400	334542	.	-	.	Parent=ENST00000592722
+19	track name	exon	336083	336173	.	-	.	Parent=ENST00000592722
+19	track name	exon	340514	340599	.	-	.	Parent=ENST00000592722
+19	track name	transcript	334115	344798	.	-	.	ID=ENST00000587966;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-002
+19	track name	exon	334115	334542	.	-	.	Parent=ENST00000587966
+19	track name	exon	344774	344798	.	-	.	Parent=ENST00000587966
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