--- a/bismark_bowtie2_wrapper.xml	Thu Aug 01 10:47:13 2019 -0400
+++ b/bismark_bowtie2_wrapper.xml	Wed Aug 21 12:59:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy2" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy3" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
         <requirement type="package" version="0.22.1">bismark</requirement>
@@ -119,9 +119,6 @@
             ## default 2
             --max-reseed $params.max_reseed
 
-            ## default 70
-            ##--maqerr $params.maqerr
-
             ## default unlimited
             #if $params.qupto != 0:
                 --qupto $params.qupto
@@ -130,6 +127,10 @@
                 --skip-reads $params.skip_reads
             #end if
 
+            #if $params.score_min != "":
+                --score-min '${params.score_min}'
+            #end if
+
             ## if set, disable the original behaviour
             $params.no_mixed
             ## if set, disable the original behaviour
@@ -252,9 +253,7 @@
                 <!-- -L -->
                 <param name="seed_len" type="integer" value="20"
                        label="Length of the seed substrings to align during multiseed alignment"/>
-                <!--
-                <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
-                -->
+
                 <!-- -D -->
                 <param name="seed_extention_attempts" type="integer" value="15"
                        label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
@@ -268,6 +267,8 @@
                 <param name="skip_reads" type="integer" value="0"
                        label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
 
+                <param argument="--score-min" name="score_min" type="text" value="" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="This is a function of read length. For instance, specifying `L,0,-0.2` sets the minimum-score function `f` to `f(x) = 0 + -0.2 * x`, where `x` is the read length."/>
+
                 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
                        label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
                        help=""/>
@@ -511,6 +512,38 @@
             <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>
+        <test>
+            <param name="genomeSource" value="history"/>
+            <param name="own_file" value="mm10.tiny.fa.gz" />
+            <param name="sPaired" value="single"/>
+            <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
+            <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"/>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="score_min" value="L,0,-0.8" />
+            </conditional>
+
+            <output name="output_stdout" file="summary_custom.txt" ftype="txt" lines_diff="94">
+                 <assert_contents>
+                     <has_text text="Sequences analysed in total:" />
+                     <has_text text="44115" />
+                     <has_text text="Mapping efficiency:" />
+                     <has_text text="4.5%" />
+                     <has_text text="Bismark run complete" />
+                 </assert_contents>
+            </output>
+            <output name="report_file" file="mapping_report_custom.txt" ftype="txt" lines_diff="6"/>
+            <output name="output" file="mapped_reads_custom.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
+
+            <assert_command>
+                <has_text text="--score-min 'L,0,-0.8'" />
+            </assert_command>
+        </test>
     </tests>
 
     <help>