# HG changeset patch
# User iuc
# Date 1618002909 0
# Node ID 03b7b7811ea64089a24d24935dd1c877b9d99217
# Parent  57dc46adf2da743b2559534f22b3673f55e9d75b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"

diff -r 57dc46adf2da -r 03b7b7811ea6 flair_collapse.xml
--- a/flair_collapse.xml	Fri Nov 27 21:56:08 2020 +0000
+++ b/flair_collapse.xml	Fri Apr 09 21:15:09 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@" profile="20.01">
+<tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@+galaxy0" profile="20.01">
     <description>defines high-confidence isoforms from flair-corrected reads</description>
 
     <macros>
@@ -56,7 +56,7 @@
     ]]></command>
     <inputs>
         <param name="input_query" argument="-q" type="data" format="bed" label="Corrected Reads as BED file"/>
-        <param name="input_reads" argument="-r" type="data" format="fasta,fastq" label="FASTA/FASTQ file of raw reads"/>
+        <param name="input_reads" argument="-r" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="FASTA/FASTQ file of raw reads"/>
         <expand macro="reference_interface" />
         <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
         <param name="input_promotors" optional="true" argument="-p" type="data" format="bed" label="Promotor BED file to identify full-length reads" />
diff -r 57dc46adf2da -r 03b7b7811ea6 flair_macros.xml
--- a/flair_macros.xml	Fri Nov 27 21:56:08 2020 +0000
+++ b/flair_macros.xml	Fri Apr 09 21:15:09 2021 +0000
@@ -13,10 +13,17 @@
 
     <token name="@PREPARE_REF@"><![CDATA[
         #if str($reference_source_genome.ref_selector_genome) == 'history':
-            ln -s '$reference_source_genome.reffile' reference.fa &&
+            #set reference = $reference_source_genome.reffile
+            #set ext = $reference.ext
             samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 &&
         #else
-            ln -s '${reference_source_genome.reffile.fields.path}' reference.fa &&
+            #set reference = $reference_source_genome.reffile.fields.path
+            #set ext = $reference_source_genome.reffile.fields.path
+        #end if
+        #if $ext.endswith(".gz"):
+            gunzip -c '$reference' > reference.fa &&
+        #else:
+            ln -sf '$reference' reference.fa &&
         #end if
     ]]></token>
 
@@ -34,7 +41,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="reffile" argument="-g" type="data" format="fasta" label="Reference" help="Reference sequence" />
+                <param name="reffile" argument="-g" type="data" format="fasta,fasta.gz" label="Reference" help="Reference sequence" />
             </when>
         </conditional>
     </xml>