Mercurial > repos > devteam > kraken

comparison kraken.xml @ 7:19939bfcf283 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 19:41:02 -0500
parents 1496744bd2ad
children 10cb95fb0143
comparison
equal deleted inserted replaced
6:1496744bd2ad 7:19939bfcf283
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken" name="Kraken" version="1.1.2"> 2 <tool id="kraken" name="Kraken" version="1.1.3">
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>
8 </macros> 8 </macros>
9 <expand macro="requirements" />
10 <expand macro="stdio" />
11 <expand macro="version_command" />
9 <command> 12 <command>
10 <![CDATA[ 13 <![CDATA[
11 @SET_DATABASE_PATH@ && 14 @SET_DATABASE_PATH@ &&
12 kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ 15 kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@
13 16
45 #end if 48 #end if
46 49
47 #if $split_reads: 50 #if $split_reads:
48 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}" 51 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
49 #end if 52 #end if
50 --output "${output}" 53
54 ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3
55
56 > "${output}"
51 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" 57 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
52 ]]> 58 ]]>
53 </command> 59 </command>
54 <inputs> 60 <inputs>
55 <conditional name="single_paired"> 61 <conditional name="single_paired">
56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> 62 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
57 <option value="collection">Collection</option> 63 <option value="collection">Collection</option>
58 <option value="yes">Yes</option> 64 <option value="yes">Paired</option>
59 <option selected="True" value="no">No</option> 65 <option selected="True" value="no">Single</option>
60 </param> 66 </param>
61 <when value="collection"> 67 <when value="collection">
62 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" /> 68 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" />
63 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> 69 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
64 </when> 70 </when>
99 <filter>(split_reads)</filter> 105 <filter>(split_reads)</filter>
100 </data> 106 </data>
101 <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" /> 107 <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
102 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> 108 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
103 </outputs> 109 </outputs>
110
111 <tests>
112 <test>
113 <param name="single_paired_selector" value="no"/>
114 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
115 <param name="split_reads" value="false"/>
116 <param name="quick" value="no"/>
117 <param name="only-classified-output" value="false"/>
118 <param name="kraken_database" value="test_db"/>
119 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
120 </test>
121 </tests>
104 <help> 122 <help>
105 <![CDATA[ 123 <![CDATA[
106 **What it does** 124 **What it does**
107 125
108 Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise. 126 Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.
140 c) the next 31 k-mers contained an ambiguous nucleotide 158 c) the next 31 k-mers contained an ambiguous nucleotide
141 d) the next k-mer was not in the database 159 d) the next k-mer was not in the database
142 e) the last 3 k-mers mapped to taxonomy ID #562 160 e) the last 3 k-mers mapped to taxonomy ID #562
143 ]]> 161 ]]>
144 </help> 162 </help>
145 <expand macro="requirements" />
146 <expand macro="stdio" />
147 <expand macro="version_command" />
148 <expand macro="citations" /> 163 <expand macro="citations" />
149 </tool> 164 </tool>