Mercurial > repos > earlhaminst > lotus2
changeset 11:8f732780e0f3 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
| author | earlhaminst |
|---|---|
| date | Tue, 08 Jun 2021 19:53:13 +0000 |
| parents | 6d55d9464719 |
| children | 3f3ee496acec |
| files | lotus2.xml test-data/mapping_paired.txt |
| diffstat | 2 files changed, 28 insertions(+), 39 deletions(-) [+] |
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--- a/lotus2.xml Tue Jun 08 17:21:29 2021 +0000 +++ b/lotus2.xml Tue Jun 08 19:53:13 2021 +0000 @@ -41,49 +41,21 @@ <command detect_errors="exit_code"><![CDATA[ #import os.path #import re -#def symlink_basename($f, $f_ext): - #set $fn = re.sub('[^\w\-_.]', '_', $f.element_identifier) - #if $fn.endswith('.gz'): - #set $fn = $fn[:-3] - #end if - #if $f_ext.startswith('fastq'): - #set $exts_to_drop = ('.fq', '.fastq', '.fastqsanger') - #elif $f_ext.startswith('fasta'): - #set $exts_to_drop = ('.fa', '.fasta', '.fna') - #else - #set $exts_to_drop = [] - #end if - #for $ext in $exts_to_drop: - #if $fn.endswith($ext): - #set $fn = $fn[:-len($ext)] - #break - #end if - #end for -$fn#slurp +#def symlink_basename($f): + #set $fn = re.sub('[^\w\-_.]', '_', $f.name) +${fn}#slurp #end def mkdir input && #if $inputs.paired_or_single == 'single': #for $f in $inputs.input: - #set $ext = $f.ext.replace('sanger', '') - ln -s '$f' 'input/${symlink_basename($f, $ext)}.${ext}' && - #end for -#elif $inputs.paired_or_single == 'paired': - #for i, f in enumerate($inputs.left_input): - #set ext = $f.ext.replace('sanger', '') - ln -s '$f' 'input/input${i}.1.${ext}' && - #end for - #for $i, $f in enumerate($inputs.right_input): - #set $ext = $f.ext.replace('sanger', '') - ln -s '$f' 'input/input${i}.2.${ext}' && + ln -s '$f' 'input/${symlink_basename($f)}' && #end for #else: #for $f in $inputs.pair_input: - #set $ext = $f.forward.ext.replace('sanger', '') - ln -s '$f.forward' 'input/${symlink_basename($f, $ext)}.1.${ext}' && - #set $ext = $f.reverse.ext.replace('sanger', '') - ln -s '$f.reverse' 'input/${symlink_basename($f, $ext)}.2.${ext}' && + ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' && + ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' && #end for #end if @@ -94,9 +66,8 @@ #end if #if not $map: - lotus2 -create_map mapping.txt -i input/ && - cat mapping.txt && - #set map = 'mapping.txt' + cat '$generated_mapping' && + #set map = $generated_mapping #end if lotus2 @@ -192,7 +163,25 @@ && exit \$EXIT_VALUE ]]></command> - + <configfiles> + <configfile name="generated_mapping"><![CDATA[#slurp +#import re +#def symlink_basename($f): + #set $fn = re.sub('[^\w\-_.]', '_', $f.name) +${fn}#slurp +#end def +#SampleID fastqFile SequencingRun +#if $inputs.paired_or_single == 'single': + #for $i, $f in enumerate($inputs.input): +SMPL${i} ${symlink_basename($f)} a + #end for +#else: + #for $i, $f in enumerate($inputs.pair_input): +SMPL${i} ${symlink_basename($f.forward.dataset)},${symlink_basename($f.reverse.dataset)} a + #end for +#end if +]]></configfile> + </configfiles> <inputs> <conditional name="inputs"> <param name="paired_or_single" type="select" label="Single- or Paired-end data?">