| Previous changeset 10:da8d655e2154 (2017-04-10) Next changeset 12:2ec097c8e843 (2017-04-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty |
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modified:
hisat2.xml hisat2_macros.xml |
| b |
| diff -r da8d655e2154 -r e926afbd9e10 hisat2.xml --- a/hisat2.xml Mon Apr 10 17:40:42 2017 -0400 +++ b/hisat2.xml Mon Apr 10 23:17:56 2017 -0400 |
| b |
| @@ -40,7 +40,7 @@ #if $compressed == "GZ": --un-gz '$output_unaligned_reads_l' #else if $compressed == "BZ2": - --un-gz '$output_unaligned_reads_l' + --un-bz2 '$output_unaligned_reads_l' #else: --un '$output_unaligned_reads_l' #end if |
| b |
| diff -r da8d655e2154 -r e926afbd9e10 hisat2_macros.xml --- a/hisat2_macros.xml Mon Apr 10 17:40:42 2017 -0400 +++ b/hisat2_macros.xml Mon Apr 10 23:17:56 2017 -0400 |
| b |
| @@ -62,13 +62,17 @@ #if str( $input_format.paired.unaligned_file ) == "true": #if $compressed == "GZ": --un-conc-gz '${output_unaligned_reads_l}' + #else if $compressed == "BZ2": + --un-conc-bz2 '${output_unaligned_reads_l}' #else: --un-conc '${output_unaligned_reads_l}' #end if #end if #if str( $input_format.paired.aligned_file ) == "true": #if $compressed == "GZ": - --al-conc '${output_aligned_reads_l}' + --al-conc-gz '${output_aligned_reads_l}' + #else if $compressed == "BZ2" + --al-conc-bz2 '${output_aligned_reads_l}' #else: --al-conc '${output_aligned_reads_l}' #end if @@ -98,7 +102,7 @@ #else: #set read1 = "input_f.fastq" #end if - ln -f -s "${input_format.paired.reads_f}" "${read1}" && + ln -f -s '${input_format.paired.reads_f}' ${read1} && #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"): #set read2 = "input_r.fastq.gz" @@ -109,7 +113,7 @@ #else: #set read2 = "input_r.fastq" #end if - ln -f -s "${input_format.paired.reads_r}" "${read2}" && + ln -f -s '${input_format.paired.reads_r}' ${read2} && #else if str($input_format.paired.paired_selector) == 'paired_collection': #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" @@ -120,7 +124,7 @@ #else: #set read1 = "input_f.fastq" #end if - ln -s "${input_format.paired.reads.forward}" "${read1}" && + ln -s '${input_format.paired.reads.forward}' ${read1} && #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): #set read2 = "input_r.fastq.gz" @@ -131,7 +135,7 @@ #else: #set read2 = "input_r.fastq" #end if - ln -s "${input_format.paired.reads.reverse}" "${read2}" && + ln -s '${input_format.paired.reads.reverse}' ${read2} && #else: #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" @@ -142,7 +146,7 @@ #else: #set read1 = "input_f.fastq" #end if - ln -s "${input_format.paired.reads}" "${read1}" && + ln -s '${input_format.paired.reads}' ${read1} && #end if ]]> </token> |