diff bismark_bowtie2_wrapper.xml @ 21:120b7b35e442 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"

--- a/bismark_bowtie2_wrapper.xml	Fri Oct 04 11:33:27 2019 -0400
+++ b/bismark_bowtie2_wrapper.xml	Thu Apr 22 17:05:46 2021 +0000
@@ -315,8 +315,8 @@
                        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"
-                       truevalue="--non-directional" falsevalue="" checked="false"
+                <param argument="--non_directional" name="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"
                        truevalue="--pbat" falsevalue="" checked="false"
@@ -549,6 +549,37 @@
         <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>
+            <repeat name="mate_list">
+                <param name="input_mate1" value="input2.fq" ftype="fastqsanger"/>
+                <param name="input_mate2" value="input2.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_two_samples.txt" ftype="txt" lines_diff="94">
+                 <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_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>
+            <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"/>