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comparison metamlst.xml @ 1:4d3e54bace61 draft default tip

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty"
author thanhlv
date Wed, 23 Feb 2022 22:57:02 +0000
parents d1df295495a9
children
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0:d1df295495a9 1:4d3e54bace61
40 #else: 40 #else:
41 #set read2 = $name_1 + '.fastq' 41 #set read2 = $name_1 + '.fastq'
42 #end if 42 #end if
43 ln -f -s '${library.input_2}' ${read2} && 43 ln -f -s '${library.input_2}' ${read2} &&
44 #else if str($library.type) == 'paired_collection': 44 #else if str($library.type) == 'paired_collection':
45 #set pe_input_1 = $library.input_1.forward 45 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.input_1.forward.name)) + "_1"
46 #set pe_input_2 = $library.input_1.reverse 46 #set name_2 = re.sub('[^\w\-\s]', '_', str($library.input_1.reverse.name)) + "_2"
47 #set name_1 = re.sub('[^\w\-\s]', '_', str($library.pe_input_1.name)) + "_1"
48 #set name_2 = re.sub('[^\w\-\s]', '_', str($library.pe_input_2.name)) + "_2"
49 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): 47 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
50 #set read1 = $name_1 + '.fastq.gz' 48 #set read1 = $name_1 + '.fastq.gz'
51 #set compressed = "GZ" 49 #set compressed = "GZ"
52 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): 50 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
53 #set read1 = $name_1 + '.fastq.bz2' 51 #set read1 = $name_1 + '.fastq.bz2'
149 metamlst-merge.py ./out -d '$metamlstdb.fields.path' && 147 metamlst-merge.py ./out -d '$metamlstdb.fields.path' &&
150 #if $log 148 #if $log
151 cat ./out/*.out > log.txt && 149 cat ./out/*.out > log.txt &&
152 #end if 150 #end if
153 #if $write_sequences 151 #if $write_sequences
154 cat ./out/*.nfo > sequences.txt 152 cat ./out/*.nfo > sequences.txt &&
155 #end if 153 #end if
154 echo "Finished"
156 ]]> </command> 155 ]]> </command>
157 156
158 <inputs> 157 <inputs>
159 <conditional name="library"> 158 <conditional name="library">
160 <param name="type" type="select" label="Is this single or paired library"> 159 <param name="type" type="select" label="Is this single or paired library">