--- a/bismark_bowtie2_wrapper.xml	Tue Jul 30 06:30:36 2019 -0400
+++ b/bismark_bowtie2_wrapper.xml	Tue Jul 30 10:33:02 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy1" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
         <requirement type="package" version="0.22.1">bismark</requirement>
@@ -6,6 +6,8 @@
         <requirement type="package" version="2.3.5">bowtie2</requirement>
     </requirements>
     <command><![CDATA[
+        #import re
+
         #if $singlePaired.sPaired == "single":
             #if $singlePaired.input_singles.ext == "fasta":
                 #set read1 = 'input_1.fa'
@@ -19,26 +21,27 @@
             #set $mate1 = list()
             #set $mate2 = list()
             #for $mate_pair in $singlePaired.mate_list
-                $mate1.append( str($mate_pair.input_mate1) )
-                $mate2.append( str($mate_pair.input_mate2) )
 
                 #if $mate_pair.input_mate1.ext == "fasta":
-                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fa'
+                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
                 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
-                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq.gz'
+                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
                 #else
-                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq'
+                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
                 #end if
                 ln -s '${mate_pair.input_mate1}' ${read1} &&
 
                 #if $mate_pair.input_mate2.ext == "fasta":
-                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fa'
+                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
                 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
-                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq.gz'
+                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
                 #else
-                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq'
+                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
                 #end if
                 ln -s '${mate_pair.input_mate2}' ${read2} &&
+
+                $mate1.append( str($read1) )
+                $mate2.append( str($read2) )
             #end for
         #end if
 
@@ -481,6 +484,33 @@
             <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/>
             <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
         </test>
+        <test>
+            <param name="genomeSource" value="history"/>
+            <param name="own_file" value="mm10.tiny.fa.gz" />
+            <param name="sPaired" value="paired"/>
+            <repeat name="mate_list">
+                <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/>
+                <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/>
+            </repeat>
+            <param name="sort_bam" value="false"/>
+            <param name="settingsType" value="custom"/>
+            <param name="suppressed_read_file" value="true"/>
+            <param name="unmapped_read_file" value="true"/>
+            <param name="bismark_stdout" value="true"/>
+            <param name="isReportOutput" value="true"/>
+
+            <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="80">
+                 <assert_contents>
+                     <has_text text="Sequence pairs analysed in total:" />
+                     <has_text text="1000" />
+                     <has_text text="Mapping efficiency:" />
+                     <has_text text="0.0%" />
+                     <has_text text="Bismark run complete" />
+                 </assert_contents>
+            </output>
+            <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/>
+            <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
+        </test>
     </tests>
 
     <help>