Mercurial > repos > bgruening > bismark
diff bismark_bowtie2_wrapper.xml @ 19:359f8b60d316 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
| author | bgruening |
|---|---|
| date | Fri, 04 Oct 2019 07:54:51 -0400 |
| parents | aa9bf0f29a9f |
| children | 120b7b35e442 |
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--- a/bismark_bowtie2_wrapper.xml Tue Oct 01 12:43:53 2019 -0400 +++ b/bismark_bowtie2_wrapper.xml Fri Oct 04 07:54:51 2019 -0400 @@ -12,7 +12,7 @@ #if $singlePaired.input_singles.ext == "fasta": #set read1 = 'input_1.fa' #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: - #if $params.pbat == "--pbat" + #if $params.settingsType == "custom" and $params.pbat == "--pbat" #set read1 = 'input_1.fq' #else #set read1 = 'input_1.fq.gz' @@ -21,7 +21,7 @@ #set read1 = 'input_1.fq' #end if - #if $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: + #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: zcat '${singlePaired.input_singles}' > '${read1}' && #else ln -s '${singlePaired.input_singles}' '${read1}' && @@ -34,7 +34,7 @@ #if $mate_pair.input_mate1.ext == "fasta": #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa' #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: - #if $params.pbat == "--pbat" + #if $params.settingsType == "custom" and $params.pbat == "--pbat" #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' #else #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' @@ -43,7 +43,7 @@ #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' #end if - #if $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: + #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: zcat '${mate_pair.input_mate1}' > '${read1}' && #else ln -s '${mate_pair.input_mate1}' '${read1}' && @@ -52,7 +52,7 @@ #if $mate_pair.input_mate2.ext == "fasta": #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa' #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: - #if $params.pbat == "--pbat" + #if $params.settingsType == "custom" and $params.pbat == "--pbat" #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' #else #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' @@ -61,7 +61,7 @@ #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' #end if - #if $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: + #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: zcat '${mate_pair.input_mate2}' > '${read2}' && #else ln -s '${mate_pair.input_mate2}' '${read2}' &&