Update bismark_bowtie2_wrapper.xml

added expect_num_outputs to tests

removed redundant name Attributes from score_min, non_directional, pbat and local

tools/bismark/bismark_bowtie2_wrapper.xml

@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy5" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy4" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
         <requirement type="package" version="0.22.1">bismark</requirement>
@@ -298,7 +298,7 @@
                 <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 argument="--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)"
@@ -317,14 +317,14 @@
                        label="Write the bismark output and summary information to an extra file"/>
                 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
                        label="Offer all report files concatenated in one file (Mapping Report)"/>
-                <param argument="--non_directional" name="non_directional" type="boolean"
+                <param argument="--non_directional" type="boolean"
                        truevalue="--non_directional" falsevalue="" checked="false"
                        label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>
-                <param argument="--pbat" name="pbat" type="boolean"
+                <param argument="--pbat" type="boolean"
                        truevalue="--pbat" falsevalue="" checked="false"
                        label="Treat input data as PBAT-Seq libraries"
                        help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." />
-                <param argument="--local" name="local" type="boolean"
+                <param argument="--local" type="boolean"
                        truevalue="--local" falsevalue="" checked="false"
                        label="Allow local alignments"
                        help="In this mode, it is not required that the entire read aligns from one end to the other. Rather, some characters may be omitted (“soft-clipped”) from the ends." />
@@ -477,7 +477,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genomeSource" value="history"/>
             <param name="own_file" value="mm10.tiny.fa.gz" />
             <param name="sPaired" value="single"/>
@@ -501,7 +501,7 @@
             <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
             <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genomeSource" value="history"/>
             <param name="own_file" value="mm10.tiny.fa.gz" />
             <param name="sPaired" value="single"/>
@@ -525,7 +525,7 @@
             <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>
+        <test expect_num_outputs="3">
             <param name="genomeSource" value="history"/>
             <param name="own_file" value="mm10.tiny.fa.gz" />
             <param name="sPaired" value="paired"/>
@@ -552,7 +552,7 @@
             <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>
+        <test expect_num_outputs="3">
             <param name="genomeSource" value="history"/>
             <param name="own_file" value="mm10.tiny.fa.gz" />
             <param name="sPaired" value="paired"/>
@@ -583,7 +583,7 @@
             <output name="report_file" file="mapping_report_mate_two_samples.txt" ftype="txt" lines_diff="12"/>
             <output name="output" file="mapped_reads_mate_two_samples.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genomeSource" value="history"/>
             <param name="own_file" value="mm10.tiny.fa.gz" />
             <param name="sPaired" value="single"/>
@@ -615,7 +615,7 @@
                 <has_text text="--score-min 'L,0,-0.8'" />
             </assert_command>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genomeSource" value="history"/>
             <param name="own_file" value="mm10.tiny.fa.gz" />
             <param name="sPaired" value="single"/>
@@ -646,6 +646,7 @@
             <assert_command>
                 <has_text text="--pbat" />
             </assert_command>
+
         </test>
     </tests>