# HG changeset patch
# User dfornika
# Date 1578514254 0
# Node ID 77b64aa5592b8a80f90b4d5495cdb398b28cb723
# Parent  033e0a3674bcff81d966f493157c3bdfa5bb6d19
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"

diff -r 033e0a3674bc -r 77b64aa5592b micall_lite.xml
--- a/micall_lite.xml	Mon Jan 06 23:49:32 2020 +0000
+++ b/micall_lite.xml	Wed Jan 08 20:10:54 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
+<tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy1">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -12,35 +12,35 @@
           #if str( $fastq_input.fastq_input_selector ) == "paired":
             #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
               #set unzipped = False
-              #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq.gz'
+              #set reads1 = $fastq_input.reads1.name + '_R1.fastq.gz'
             #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
               #set unzipped = True
-              #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq'
+              #set reads1 = $fastq_input.reads1.name + '_R1.fastq'
             #end if
             ln -s '$fastq_input.reads1' '$reads1' &&
             #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
               #set unzipped = False
-              #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq.gz'
+              #set reads2 = $fastq_input.reads2.name + '_R2.fastq.gz'
             #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
               #set unzipped = True
-              #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq'
+              #set reads2 = $fastq_input.reads2.name + '_R2.fastq'
             #end if
             ln -s '$fastq_input.reads2' '$reads2' &&
           #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
             #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
               #set unzipped = False
-              #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq.gz'
+              #set reads1 = $fastq_input.pair.name + '_R1.fastq.gz'
             #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
               #set unzipped = True
-              #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq'
+              #set reads1 = $fastq_input.pair.name + '_R1.fastq'
             #end if
             ln -s '$fastq_input.pair.forward' '$reads1' &&
             #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
               #set unzipped = False
-              #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq.gz'
+              #set reads2 = $fastq_input.pair.name + '_R2.fastq.gz'
             #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
               #set unzipped = True
-              #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq'
+              #set reads2 = $fastq_input.pair.name + '_R2.fastq'
             #end if
             ln -s '$fastq_input.pair.reverse' '$reads2' &&
           #end if