diff bismark_bowtie2_wrapper.xml @ 13:f211753166bd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d

--- a/bismark_bowtie2_wrapper.xml	Wed Jun 05 07:44:26 2019 -0400
+++ b/bismark_bowtie2_wrapper.xml	Tue Jul 30 06:30:36 2019 -0400
@@ -1,11 +1,47 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.3" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
-        <requirement type="package" version="0.20.0">bismark</requirement>
+        <requirement type="package" version="0.22.1">bismark</requirement>
         <requirement type="package" version="1.8">samtools</requirement>
-        <requirement type="package" version="2.3.4.2">bowtie2</requirement>
+        <requirement type="package" version="2.3.5">bowtie2</requirement>
     </requirements>
     <command><![CDATA[
+        #if $singlePaired.sPaired == "single":
+            #if $singlePaired.input_singles.ext == "fasta":
+                #set read1 = 'input_1.fa'
+            #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
+                #set read1 = 'input_1.fq.gz'
+            #else
+                #set read1 = 'input_1.fq'
+            #end if
+            ln -s '${singlePaired.input_singles}' ${read1} &&
+        #else:
+            #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'
+                #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'
+                #else
+                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq'
+                #end if
+                ln -s '${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'
+                #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'
+                #else
+                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq'
+                #end if
+                ln -s '${mate_pair.input_mate2}' ${read2} &&
+            #end for
+        #end if
+
         python '$__tool_directory__/bismark_wrapper.py'
 
         ## Change this to accommodate the number of threads you have available.
@@ -29,7 +65,7 @@
         ##
 
         #if $singlePaired.sPaired == "single":
-            --single-paired '$singlePaired.input_singles'
+            --single-paired '${read1}'
 
             #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]:
                 --phred64-quals
@@ -41,12 +77,6 @@
             #end if
         #else:
             --mate-paired
-            #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) )
-            #end for
 
             --mate1 #echo ','.join($mate1)
             --mate2 #echo ','.join($mate2)
@@ -407,7 +437,7 @@
             <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.gz" ftype="fastqsanger"/>
+            <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"/>
@@ -427,6 +457,30 @@
             <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>
+            <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" ftype="fastqsanger"/>
+            <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_short.txt" ftype="txt" lines_diff="80">
+                 <assert_contents>
+                     <has_text text="Sequences analysed in total:" />
+                     <has_text text="1000" />
+                     <has_text text="Mapping efficiency:" />
+                     <has_text text="0.8%" />
+                     <has_text text="Bismark run complete" />
+                 </assert_contents>
+            </output>
+            <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>
     </tests>
 
     <help>