# HG changeset patch
# User bgruening
# Date 1570190091 14400
# Node ID 359f8b60d316702c32fe92f1b20e3708a9042d83
# Parent  bb74e17e47d72489fad027bf46d2bde621925a4a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"

diff -r bb74e17e47d7 -r 359f8b60d316 bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml	Tue Oct 01 12:43:53 2019 -0400
+++ b/bismark_bowtie2_wrapper.xml	Fri Oct 04 07:54:51 2019 -0400
@@ -12,7 +12,7 @@
             #if $singlePaired.input_singles.ext == "fasta":
                 #set read1 = 'input_1.fa'
             #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
-                #if $params.pbat == "--pbat"
+                #if $params.settingsType == "custom" and $params.pbat == "--pbat"
                     #set read1 = 'input_1.fq'
                 #else
                     #set read1 = 'input_1.fq.gz'
@@ -21,7 +21,7 @@
                 #set read1 = 'input_1.fq'
             #end if
 
-            #if $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
+            #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
                 zcat '${singlePaired.input_singles}' > '${read1}' &&
             #else
                 ln -s '${singlePaired.input_singles}' '${read1}' &&
@@ -34,7 +34,7 @@
                 #if $mate_pair.input_mate1.ext == "fasta":
                     #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
                 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
-                    #if $params.pbat == "--pbat"
+                    #if $params.settingsType == "custom" and $params.pbat == "--pbat"
                         #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
                     #else
                         #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
@@ -43,7 +43,7 @@
                     #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
                 #end if
 
-                #if $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
+                #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
                     zcat '${mate_pair.input_mate1}' > '${read1}' &&
                 #else
                     ln -s '${mate_pair.input_mate1}' '${read1}' &&
@@ -52,7 +52,7 @@
                 #if $mate_pair.input_mate2.ext == "fasta":
                     #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
                 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
-                    #if $params.pbat == "--pbat"
+                    #if $params.settingsType == "custom" and $params.pbat == "--pbat"
                         #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
                     #else
                         #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
@@ -61,7 +61,7 @@
                     #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
                 #end if
 
-                #if $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
+                #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
                     zcat '${mate_pair.input_mate2}' > '${read2}' &&
                 #else
                     ln -s '${mate_pair.input_mate2}' '${read2}' &&