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comparison kraken2.xml @ 6:6a9137c96822 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty
author dfornika
date Mon, 04 Mar 2019 16:57:25 -0500
parents babd549eeb44
children 7b9218c5e126
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5:df49a08d5b95 6:6a9137c96822
9 <version_command>kraken2 --version</version_command> 9 <version_command>kraken2 --version</version_command>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 kraken2 12 kraken2
13 --threads \${GALAXY_SLOTS:-1} 13 --threads \${GALAXY_SLOTS:-1}
14 @INPUT_DATABASE@
15 #if $single_paired.single_paired_selector == 'yes' 14 #if $single_paired.single_paired_selector == 'yes'
16 #if $forward_input.is_of_type( 'fastq' ): 15 #if $forward_input.is_of_type( 'fastq' ):
17 --fastq-input 16 --fastq-input
18 #else: 17 #else:
19 --fasta-input 18 --fasta-input
34 #else: 33 #else:
35 --fasta-input 34 --fasta-input
36 #end if 35 #end if
37 '${single_paired.input_sequences}' 36 '${single_paired.input_sequences}'
38 #end if 37 #end if
39 --db '$database' 38 --db '$kraken2_database'
40 > '$output' 39 > '$output'
41 ]]> 40 ]]>
42 </command> 41 </command>
43 <inputs> 42 <inputs>
44 <conditional name="single_paired"> 43 <conditional name="single_paired">
58 </when> 57 </when>
59 <when value="no"> 58 <when value="no">
60 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> 59 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
61 </when> 60 </when>
62 </conditional> 61 </conditional>
63 <param name="kmer_db" type="select"> 62 <param name="kraken2_database" type="select">
64 <options from_data_table="kraken2_databases"> 63 <options from_data_table="kraken2_databases">
65 <validator type="no_options" message="No Kraken2 databases are available" /> 64 <validator type="no_options" message="No Kraken2 databases are available" />
66 </options> 65 </options>
67 </param> 66 </param>
68 </inputs> 67 </inputs>