Mercurial > repos > bgruening > bismark
diff bismark_bowtie2_wrapper.xml @ 13:f211753166bd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
author | bgruening |
---|---|
date | Tue, 30 Jul 2019 06:30:36 -0400 |
parents | 1f15ad5ca867 |
children | b6aa3b6ba129 |
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--- 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>