diff gffread.xml @ 7:4dea02886337 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432"

--- 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"/>