# HG changeset patch
# User public-health-bioinformatics
# Date 1578523398 18000
# Node ID bb549c5eaf34d1e844e98006908b90e2b9cfdd53
# Parent  023064145beaa45355d7b5e3832584830dd5bda4
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"

diff -r 023064145bea -r bb549c5eaf34 micall_lite.xml
--- a/micall_lite.xml	Mon Jan 06 19:10:15 2020 -0500
+++ b/micall_lite.xml	Wed Jan 08 17:43:18 2020 -0500
@@ -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