Mercurial > repos > iuc > nanoplot
changeset 8:a02b8b3f5a0c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit af418b2445709e63d3ed744f93fe74559e4fbaff
| author | iuc |
|---|---|
| date | Wed, 10 Apr 2024 14:30:37 +0000 |
| parents | 7b379e98b9a9 |
| children | a38bdcec9e4c |
| files | nanoplot.xml |
| diffstat | 1 files changed, 11 insertions(+), 38 deletions(-) [+] |
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--- a/nanoplot.xml Thu Mar 07 08:46:06 2024 +0000 +++ b/nanoplot.xml Wed Apr 10 14:30:37 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="22.05"> +<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1" profile="22.05"> <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description> <macros> <token name="@TOOL_VERSION@">1.42.0</token> @@ -16,47 +16,20 @@ </stdio--> <version_command>NanoPlot --version</version_command> <command detect_errors="exit_code"><![CDATA[ -## set TMPDIR if not already set by admin -## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0` -## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}; - -#set $myfiles = $mode.reads.files +#set $myfiles = $mode.reads.files if $mode.choice == 'combined' else [$mode.reads.files] #set reads_temp = [] -#if $mode.choice == 'combined': - #for $i, $f in enumerate($myfiles) - #if $f.ext.startswith("fastq"): - #set $extension = 'fastq' - #else - #set $extension = $f.ext - #end if - #if $f.ext.endswith(".gz"): - #set $f = $extension + ".gz" - #else if $f.ext.endswith(".bz"): - #set $extension = $extension + "bz2" - #end if - ln -s '$f' './read_${i}.$extension' && - #if "bam" in $extension - ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' && - #end if - $reads_temp.append("read_" + str($i) + "." + str($extension)) - #end for -#else - #if $myfiles.ext.startswith("fastq"): - #set $extension = 'fastq' +#for $i, $f in enumerate($myfiles) + #if $f.ext.startswith("fastq"): + #set $extension = "fastq" if "." not in $f.ext else "fastq.%s" % $f.ext.split(".")[-1] #else - #set $extension = $myfiles.ext - #end if - #if $myfiles.ext.endswith(".gz"): - #set $extension = $extension + ".gz" - #else if $myfiles.ext.endswith(".bz"): - #set $extension = $extension + "bz2" + #set $extension = $f.ext #end if - ln -s '$myfiles' './read.$extension' && - #if "bam" in $extension - ln -s '$myfiles.metadata.bam_index' './read.${extension}.bai' && + ln -s '$f' './read_${i}.$extension' && + #if $extension == "bam" + ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' && #end if - $reads_temp.append("read." + str($extension)) -#end if + $reads_temp.append("read_" + str($i) + "." + str($extension)) +#end for NanoPlot --threads \${GALAXY_SLOTS:-4}