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comparison mitokmer.xml @ 7:56b71adcaba7 draft

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planemo upload commit acd0f9df0a6b4aacd9c53c73e3b8e94dd36ee3dc
author galaxytrakr
date Tue, 15 Sep 2026 22:25:19 +0000
parents e4d4fc748584
children 2b1f3db24c25
comparison
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6:e4d4fc748584 7:56b71adcaba7
1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.22" profile="21.05"> 1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.23" profile="21.05">
2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description> 2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description>
3 <requirements> 3 <requirements>
4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container> 4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container>
5 </requirements> 5 </requirements>
6 6
21 ln -sf /usr/local/bin/kmerread7 ./kmerread7 && 21 ln -sf /usr/local/bin/kmerread7 ./kmerread7 &&
22 22
23 ## ── Stage input reads and build jobs file ──────────────────────────── 23 ## ── Stage input reads and build jobs file ────────────────────────────
24 #if $reads.reads_type == "single" 24 #if $reads.reads_type == "single"
25 mkdir -p ./reads && 25 mkdir -p ./reads &&
26 #set sample_name = $reads.input.name.replace(' ', '_') 26 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
27 #set read_count = 0 27 #set read_count = 0
28 #for $read in $reads.input 28 #for $read in $reads.input
29 #set ext = $fix_ext($read.ext) 29 #set ext = $fix_ext($read.ext)
30 #set fname = re.sub('[^\w\-_.]', '_', $read.element_identifier) + '.' + $ext 30 #set fname = re.sub('[^\w\-_.]', '_', $read.element_identifier) + '.' + $ext
31 ln -sf '$read' './reads/${fname}' && 31 ln -sf '$read' './reads/${fname}' &&
38 printf '%s\n' './reads/${fname}' >> ./jobs7m/jobs7m.txt && 38 printf '%s\n' './reads/${fname}' >> ./jobs7m/jobs7m.txt &&
39 #end for 39 #end for
40 #else 40 #else
41 ## paired collection: forward + reverse 41 ## paired collection: forward + reverse
42 mkdir -p ./reads && 42 mkdir -p ./reads &&
43 #set sample_name = $reads.input.name.replace(' ', '_') 43 #set sample_name = re.sub('[^\w\-_.]', '_', $reads.input.name)
44 #set fwd_ext = $fix_ext($reads.input.forward.ext) 44 #set fwd_ext = $fix_ext($reads.input.forward.ext)
45 #set rev_ext = $fix_ext($reads.input.reverse.ext) 45 #set rev_ext = $fix_ext($reads.input.reverse.ext)
46 #set base = re.sub('[^\w\-_.]', '_', $reads.input.element_identifier) 46 #set base = re.sub('[^\w\-_.]', '_', $reads.input.element_identifier)
47 #set fwd_fname = $base + '_1.' + $fwd_ext 47 #set fwd_fname = $base + '_1.' + $fwd_ext
48 #set rev_fname = $base + '_2.' + $rev_ext 48 #set rev_fname = $base + '_2.' + $rev_ext