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comparison kraken.xml @ 1:7b3ef9b4af80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
author devteam
date Wed, 04 Nov 2015 09:47:00 -0500
parents 0f17a8816b28
children 642f30185af2
comparison
equal deleted inserted replaced
0:0f17a8816b28 1:7b3ef9b4af80
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken" name="Kraken" version="1.1.0"> 2 <tool id="kraken" name="Kraken" version="1.1.1">
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>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 @SET_DATABASE_PATH@ && 11 @SET_DATABASE_PATH@ &&
12 kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ 12 kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@
13 13
14 #if $input_sequences.is_of_type( 'fastq' ):
15 --fastq-input
16 #else:
17 --fasta-input
18 #end if
19
20 ${only_classified_output} 14 ${only_classified_output}
21 15
22 #if str( $quick_operation.quick ) == "yes": 16 #if str( $quick_operation.quick ) == "yes":
23 --quick 17 --quick
24 --min-hits ${quick_operation.min_hits} 18 --min-hits ${quick_operation.min_hits}
25 19
26 #end if 20 #end if
27 21
28 "$input_sequences" 22 #if $single_paired.single_paired_selector == "yes":
23 #if $forward_input.is_of_type( 'fastq' ):
24 --fastq-input
25 #else:
26 --fasta-input
27 #end if
28 "$forward_input" "$reverse_input"
29 ${single_paired.check_names}
30 #else:
31 #if $input_sequences.is_of_type( 'fastq' ):
32 --fastq-input
33 #else:
34 --fasta-input
35 #end if
36 "$input_sequences"
37 #end if
29 38
30 #if $split_reads: 39 #if $split_reads:
31 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}" 40 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
32 #end if 41 #end if
33 --output "${output}" 42 --output "${output}"
34 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" 43 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
35 ]]> 44 ]]>
36 </command> 45 </command>
37 <inputs> 46 <inputs>
38 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> 47 <conditional name="single_paired">
48 <param name="single_paired_selector" type="select" label="Reads are paired-end" help="--paired">
49 <option value="yes">Yes</option>
50 <option selected="True" value="no">No</option>
51 </param>
52 <when value="yes">
53 <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"/>
55 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
56 </when>
57 <when value="no">
58 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
59 </when>
60
61 </conditional>
39 <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/> 62 <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/>
40 63
41 <conditional name="quick_operation"> 64 <conditional name="quick_operation">
42 <param name="quick" type="select" label="Enable quick operation?" help="--quick; Rather than searching all k-mers in a sequence, stop classification after a specified number of database hit"> 65 <param name="quick" type="select" label="Enable quick operation?" help="--quick; Rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
43 <option value="yes">Yes</option> 66 <option value="yes">Yes</option>
54 <param name="only_classified_output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences" help="--only-classified-output"/> 77 <param name="only_classified_output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences" help="--only-classified-output"/>
55 78
56 <expand macro="input_database" /> 79 <expand macro="input_database" />
57 </inputs> 80 </inputs>
58 <outputs> 81 <outputs>
59 <data format="tabular" label="${tool.name} on ${on_string}: Classified reads" name="classified_out"> 82 <data format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads" name="classified_out">
60 <filter>(split_reads)</filter> 83 <filter>(split_reads)</filter>
61 </data> 84 </data>
62 <data format="tabular" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out"> 85 <data format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out">
63 <filter>(split_reads)</filter> 86 <filter>(split_reads)</filter>
64 </data> 87 </data>
65 <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" /> 88 <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
66 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> 89 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
67 </outputs> 90 </outputs>