Mercurial > repos > bgruening > bismark
diff bismark_bowtie2_wrapper.xml @ 15:0b656f8c5637 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
| author | bgruening |
|---|---|
| date | Thu, 01 Aug 2019 10:47:13 -0400 |
| parents | b6aa3b6ba129 |
| children | a4504327c890 |
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--- a/bismark_bowtie2_wrapper.xml Tue Jul 30 10:33:02 2019 -0400 +++ b/bismark_bowtie2_wrapper.xml Thu Aug 01 10:47:13 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy1" profile="18.01"> +<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy2" profile="18.01"> <description>Bisulfite reads mapper</description> <requirements> <requirement type="package" version="0.22.1">bismark</requirement> @@ -16,29 +16,29 @@ #else #set read1 = 'input_1.fq' #end if - ln -s '${singlePaired.input_singles}' ${read1} && + ln -s '${singlePaired.input_singles}' '${read1}' && #else: #set $mate1 = list() #set $mate2 = list() #for $mate_pair in $singlePaired.mate_list #if $mate_pair.input_mate1.ext == "fasta": - #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa' + #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa' #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: - #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' + #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' #else - #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' + #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' #end if - ln -s '${mate_pair.input_mate1}' ${read1} && + ln -s '${mate_pair.input_mate1}' '${read1}' && #if $mate_pair.input_mate2.ext == "fasta": - #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa' + #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa' #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: - #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' + #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' #else - #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' + #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' #end if - ln -s '${mate_pair.input_mate2}' ${read2} && + ln -s '${mate_pair.input_mate2}' '${read2}' && $mate1.append( str($read1) ) $mate2.append( str($read2) ) @@ -448,7 +448,7 @@ <param name="bismark_stdout" value="true"/> <param name="isReportOutput" value="true"/> - <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80"> + <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="94"> <assert_contents> <has_text text="Sequences analysed in total:" /> <has_text text="44115" /> @@ -472,7 +472,7 @@ <param name="bismark_stdout" value="true"/> <param name="isReportOutput" value="true"/> - <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="80"> + <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="94"> <assert_contents> <has_text text="Sequences analysed in total:" /> <has_text text="1000" /> @@ -499,7 +499,7 @@ <param name="bismark_stdout" value="true"/> <param name="isReportOutput" value="true"/> - <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="80"> + <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="94"> <assert_contents> <has_text text="Sequence pairs analysed in total:" /> <has_text text="1000" />