Mercurial > repos > iuc > unicycler
changeset 12:3e44ef016b45 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit bc948510a50635ce98123c9e09ae09b39f1e5cee
| author | iuc |
|---|---|
| date | Sun, 07 Jul 2024 19:46:39 +0000 |
| parents | 8f9f06995f98 |
| children | |
| files | unicycler.xml |
| diffstat | 1 files changed, 19 insertions(+), 21 deletions(-) [+] |
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--- a/unicycler.xml Tue Dec 19 15:58:30 2023 +0000 +++ b/unicycler.xml Sun Jul 07 19:46:39 2024 +0000 @@ -2,7 +2,7 @@ <description>pipeline for bacterial genomes</description> <macros> <token name="@TOOL_VERSION@">0.5.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <edam_topics> <edam_topic>topic_0196</edam_topic> @@ -23,48 +23,46 @@ #end for ## Preparing files -#set $uncompressed = ('fastqsanger','fastq') -#set $compressed = ('fastqsanger.gz','fastq.gz') #if str( $paired_unpaired.fastq_input_selector ) == "paired" - #if $paired_unpaired.fastq_input1.file_ext in $uncompressed + #if $paired_unpaired.fastq_input1.is_of_type("fastq.gz"): + #set fq1 = "fq1.fastq.gz" + #else #set fq1 = "fq1.fastq" - #elif $paired_unpaired.fastq_input1.file_ext in $compressed - #set fq1 = "fq1.fastq.gz" #end if - #if $paired_unpaired.fastq_input2.file_ext in $uncompressed + #if $paired_unpaired.fastq_input2.is_of_type("fastq.gz"): + #set fq2 = "fq2.fastq.gz" + #else #set fq2 = "fq2.fastq" - #elif $paired_unpaired.fastq_input2.file_ext in $compressed - #set fq2 = "fq2.fastq.gz" #end if ln -s '${paired_unpaired.fastq_input1}' $fq1 && ln -s '${paired_unpaired.fastq_input2}' $fq2 && #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" - #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed + #if $paired_unpaired.fastq_input1.forward.is_of_type("fastq.gz"): + #set fq1 = "fq1.fastq.gz" + #else #set fq1 = "fq1.fastq" - #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed - #set fq1 = "fq1.fastq.gz" #end if - #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed + #if $paired_unpaired.fastq_input1.reverse.is_of_type("fastq.gz"): + #set fq2 = "fq2.fastq.gz" + #else #set fq2 = "fq2.fastq" - #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed - #set fq2 = "fq2.fastq.gz" #end if ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && #elif str( $paired_unpaired.fastq_input_selector ) == "single" - #if $paired_unpaired.fastq_input1.file_ext in $uncompressed + #if $paired_unpaired.fastq_input1.is_of_type("fastqsanger.gz"): + #set fq = "fq.fastq.gz" + #else #set fq = "fq.fastq" - #elif $paired_unpaired.fastq_input1.file_ext in $compressed - #set fq = "fq.fastq.gz" #end if ln -s '${paired_unpaired.fastq_input1}' '$fq' && #end if #if $long - #if $long.file_ext in $uncompressed + #if $long.is_of_type("fastq"): #set lr = "lr.fastq" - #elif $long.file_ext in $compressed + #elif $long.is_of_type("fastq.gz"): #set lr = "lr.fastq.gz" - #elif $long.is_of_type('fasta') + #elif $long.is_of_type("fasta") #set lr = "lr.fasta" #end if ln -s '${long}' '$lr' &&