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comparison kraken2.xml @ 7:7b9218c5e126 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 17:07:17 -0500
parents 6a9137c96822
children d120504e741a
comparison
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6:6a9137c96822 7:7b9218c5e126
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 --db '$kraken2_database'
14 #if $single_paired.single_paired_selector == 'yes' 15 #if $single_paired.single_paired_selector == 'yes'
15 #if $forward_input.is_of_type( 'fastq' ):
16 --fastq-input
17 #else:
18 --fasta-input
19 #end if
20 '${single_paired.forward_input}' '${single_paired.reverse_input}' 16 '${single_paired.forward_input}' '${single_paired.reverse_input}'
21 ${single_paired.check_names}
22 #elif $single_paired.single_paired_selector == "collection": 17 #elif $single_paired.single_paired_selector == "collection":
23 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
24 --fastq-input
25 #else:
26 --fasta-input
27 #end if
28 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' 18 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
29 ${single_paired.check_names}
30 #else: 19 #else:
31 #if $single_paired.input_sequences.is_of_type('fastq')
32 --fastq-input
33 #else:
34 --fasta-input
35 #end if
36 '${single_paired.input_sequences}' 20 '${single_paired.input_sequences}'
37 #end if 21 #end if
38 --db '$kraken2_database'
39 > '$output' 22 > '$output'
40 ]]> 23 ]]>
41 </command> 24 </command>
42 <inputs> 25 <inputs>
43 <conditional name="single_paired"> 26 <conditional name="single_paired">
46 <option value="yes">Paired</option> 29 <option value="yes">Paired</option>
47 <option selected="True" value="no">Single</option> 30 <option selected="True" value="no">Single</option>
48 </param> 31 </param>
49 <when value="collection"> 32 <when value="collection">
50 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" /> 33 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
51 <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
52 </when> 34 </when>
53 <when value="yes"> 35 <when value="yes">
54 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/> 36 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
55 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/> 37 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
56 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> 38 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />