diff flye.xml @ 10:75b2cf8c5aa4 draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/flye commit 2d9005e9f7366f761369b4ad7ddda383ff80a47f-dirty"

--- a/flye.xml	Mon Mar 09 14:02:16 2020 +0000
+++ b/flye.xml	Tue Mar 31 20:20:32 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="flye" name="Flye assembler" version="@VERSION@">
+<tool id="flye" name="Flye assembler" version="@VERSION@+galaxy1">
     <description>of long and error-prone reads</description>
     <macros>
         <token name="@VERSION@">2.7</token>
@@ -9,9 +9,6 @@
     <version_command>flye --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
-
-    #for $counter, $input in enumerate($inputs):
-
         #if $input.is_of_type('fastqsanger', 'fastq'):
             #set $ext = 'fastq'
         #elif $input.is_of_type('fastqsanger.gz'):
@@ -25,15 +22,10 @@
         #elif $input.is_of_type('fasta'):
             #set $ext = 'fasta'
         #end if
-        ln -s '$input' ./input_${counter}.${ext} &&
-    #end for
-
+        ln -s '$input' ./input.${ext} &&
     flye
     $mode
-    #for $counter, $input in enumerate($inputs):
-        ./input_${counter}.$ext
-    #end for
-
+    ./input.$ext
     -o out_dir
     -g '$g'
     -t \${GALAXY_SLOTS:-4}
@@ -55,7 +47,7 @@
     2>&1
     ]]>    </command>
     <inputs>
-        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads">
+        <param name="input" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="false" label="Input reads">
             <help><![CDATA[
 
     Input reads could be in FASTA or FASTQ format, uncompressed