Mercurial > repos > cstrittmatter > mitokmer
changeset 2:a0852bb4b09b draft
planemo upload commit 03463f4b0598df5619def5230de3fb758b4090ba-dirty
| author | cstrittmatter |
|---|---|
| date | Thu, 25 Apr 2019 07:59:05 -0400 |
| parents | 1434bc7b4786 |
| children | c9d98f5bc240 |
| files | mitokmer.xml |
| diffstat | 1 files changed, 36 insertions(+), 37 deletions(-) [+] |
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--- a/mitokmer.xml Mon Apr 22 09:37:19 2019 -0400 +++ b/mitokmer.xml Thu Apr 25 07:59:05 2019 -0400 @@ -5,41 +5,40 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ - #if $reads.reads_select == "paired" - #set $name = $reads.forward.name.split('.')[0].replace(' ','_') - #set $forward = $reads.forward - #set $reverse = $reads.reverse - #else - #set $name = $reads.allreads.name.split('.')[0].replace(' ','_') - #set $forward = $reads.allreads - #set $reverse = $reads.allreads - #end if + rm $__tool_directory__/R*.fastq; + #if $reads.reads_select == "paired" + #set $name = $reads.forward.name.split('.')[0].replace(' ','_') + #set $forward = $reads.forward + #set $reverse = $reads.reverse + #else + #set $name = $reads.allreads.name.split('.')[0].replace(' ','_') + #set $forward = $reads.allreads + #set $reverse = $reads.allreads + #end if echo $name; echo "-=-=-"; - #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz') - #set $fwd = "R1.fastq.gz" - #set $rev = "R2.fastq.gz" - #else if $forward.is_of_type('fastq', 'fastqsanger') - #set $fwd = "R1.fastq" - #set $rev = "R2.fastq" - #else if $forward.is_of_type('fasta.gz') - #set $fwd = "R1.fasta.gz" - #set $rev = "R2.fasta.gz" - #else - #set $fwd = "R1.fasta" - #set $rev = "R2.fasta" - #end if - ln -s $forward $__tool_directory__/process/$fwd; - ln -s $reverse $__tool_directory__/process/$rev; - #if $reads.reads_select == "single" - #set $rev = "none" - #end if - mkdir $__tool_directory__/output; - python $__tool_directory__/kmer_read_m3.py - -w $__tool_directory__/ - -d $__tool_directory__/output - -i $__tool_directory__/process/$fwd $__tool_directory__/process/$rev - + #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz') + #set $fwd = "R1.fastq.gz" + #set $rev = "R2.fastq.gz" + #else if $forward.is_of_type('fastq', 'fastqsanger') + #set $fwd = "R1.fastq" + #set $rev = "R2.fastq" + #else if $forward.is_of_type('fasta.gz') + #set $fwd = "R1.fasta.gz" + #set $rev = "R2.fasta.gz" + #else + #set $fwd = "R1.fasta" + #set $rev = "R2.fasta" + #end if + ln -s $forward $__tool_directory__/$fwd; + ln -s $reverse $__tool_directory__/$rev; + #if $reads.reads_select == "single" + #set $rev = "none" + #end if + python $__tool_directory__/kmer_read_m3.py + -w $__tool_directory__ + -d $__tool_directory__/output + -i $__tool_directory__/$fwd $__tool_directory__/$rev ]]></command> <inputs> @@ -49,7 +48,7 @@ <option value="paired">Two FASTQ datasets from your history</option> </param> <when value="single"> - <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/> + <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/> </when> <when value="paired"> <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" /> @@ -70,14 +69,14 @@ </tests> <help><![CDATA[ - + **Usage: mitokmer.py** ]]></help> <citations> <citation type="bibtex"> - meh + meh }</citation> </citations> -</tool> +</tool> \ No newline at end of file