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comparison kraken.xml @ 2:642f30185af2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:50:49 -0500
parents 7b3ef9b4af80
children 7c41dbaa9875
comparison
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1:7b3ef9b4af80 2:642f30185af2
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken" name="Kraken" version="1.1.1"> 2 <tool id="kraken" name="Kraken" version="1.1.2">
3 <description> 3 <description>
4 assign taxonomic labels to sequencing reads 4 assign taxonomic labels to sequencing reads
5 </description> 5 </description>
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
25 #else: 25 #else:
26 --fasta-input 26 --fasta-input
27 #end if 27 #end if
28 "$forward_input" "$reverse_input" 28 "$forward_input" "$reverse_input"
29 ${single_paired.check_names} 29 ${single_paired.check_names}
30 #elif $single_paired.single_paired_selector == "collection":
31 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
32 --fastq-input
33 #else:
34 --fasta-input
35 #end if
36 "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"
37 ${single_paired.check_names}
30 #else: 38 #else:
31 #if $input_sequences.is_of_type( 'fastq' ): 39 #if $input_sequences.is_of_type( 'fastq' ):
32 --fastq-input 40 --fastq-input
33 #else: 41 #else:
34 --fasta-input 42 --fasta-input
43 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" 51 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
44 ]]> 52 ]]>
45 </command> 53 </command>
46 <inputs> 54 <inputs>
47 <conditional name="single_paired"> 55 <conditional name="single_paired">
48 <param name="single_paired_selector" type="select" label="Reads are paired-end" help="--paired"> 56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
57 <option value="collection">Collection</option>
49 <option value="yes">Yes</option> 58 <option value="yes">Yes</option>
50 <option selected="True" value="no">No</option> 59 <option selected="True" value="no">No</option>
51 </param> 60 </param>
61 <when value="collection">
62 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" />
63 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
64 </when>
52 <when value="yes"> 65 <when value="yes">
53 <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/> 66 <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/>
54 <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/> 67 <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/>
55 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> 68 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
56 </when> 69 </when>