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annotate 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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1 <tool id="kraken2" name="kraken2" version="@TOOL_VERSION@+galaxy0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
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8 </requirements>
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9 <version_command>kraken2 --version</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 kraken2
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13 --threads \${GALAXY_SLOTS:-1}
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14 #if $single_paired.single_paired_selector == 'yes'
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15 #if $forward_input.is_of_type( 'fastq' ):
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16 --fastq-input
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17 #else:
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18 --fasta-input
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19 #end if
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20 '${single_paired.forward_input}' '${single_paired.reverse_input}'
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21 ${single_paired.check_names}
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22 #elif $single_paired.single_paired_selector == "collection":
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23 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
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24 --fastq-input
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25 #else:
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26 --fasta-input
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27 #end if
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28 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
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29 ${single_paired.check_names}
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30 #else:
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31 #if $single_paired.input_sequences.is_of_type('fastq')
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32 --fastq-input
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33 #else:
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34 --fasta-input
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35 #end if
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36 '${single_paired.input_sequences}'
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37 #end if
6
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38 --db '$kraken2_database'
0
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39 > '$output'
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40 ]]>
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41 </command>
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42 <inputs>
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43 <conditional name="single_paired">
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44 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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45 <option value="collection">Collection</option>
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46 <option value="yes">Paired</option>
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47 <option selected="True" value="no">Single</option>
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48 </param>
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49 <when value="collection">
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50 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
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51 <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
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52 </when>
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53 <when value="yes">
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54 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
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55 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
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56 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
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57 </when>
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58 <when value="no">
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59 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
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60 </when>
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61 </conditional>
6
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62 <param name="kraken2_database" type="select">
3
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63 <options from_data_table="kraken2_databases">
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64 <validator type="no_options" message="No Kraken2 databases are available" />
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65 </options>
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66 </param>
0
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67 </inputs>
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68 <outputs>
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69 <data name="output" format="" />
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="single_paired_selector" value="no"/>
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74 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
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75 <param name="split_reads" value="false"/>
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76 <param name="quick" value="no"/>
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77 <param name="only-classified-output" value="false"/>
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78 <param name="kraken_database" value="new_style_test_entry"/>
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79 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
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80 </test>
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81 </tests>
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82 <help>
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83 <![CDATA[
a77e88d426d9 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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84 Kraken is a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.
a77e88d426d9 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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85 ]]>
a77e88d426d9 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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86 </help>
a77e88d426d9 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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87 <expand macro="citations" />
a77e88d426d9 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
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88 </tool>