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1 <tool id="kraken" name="kraken">
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2 <description>taxonomic sequence classifier</description>
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
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5 <requirement type="package" version="0.10.5">kraken</requirement>
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6 </requirements>
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7 <command interpreter="python">kraken.py
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8 --dbtype="${databaseChoice.database}"
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9 #if $databaseChoice.database == "builtinDB":
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10 --db="${databaseChoice.builtinDatabases.fields.path}"
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11 #else:
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12 --db="NOT_SUPPORTED_YET"
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13 #end if
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14
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15 --in1="${dataFormat.input1}"
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16 #if $dataFormat.inputFormat == "pairedFastQ" or $dataFormat.inputFormat == "pairedFastA":
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17 --in2="${dataFormat.input2}"
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18 #end if
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19
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20 #if $dataFormat.inputFormat == "singleFastQ" or $dataFormat.inputFormat == "pairedFastQ":
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21 --input-format="fq"
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22 #else:
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23 --input-format="fa"
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24 #end if
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25
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26 #if $quickMode.useQuickMode == "useQuick":
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27 --quick
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28 --min-hits="${quickMode.minHits.value}"
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29 #end if
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30
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31 <!-- $output -->
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32 $kraken_summary_tsv
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33 <!-- $classified_seqs_fq
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34 $unclassified_seqs_fq -->
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35 </command>
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36 <inputs>
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37 <conditional name="databaseChoice">
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38 <param name="database" type="select" label="Do you want to use your own kraken database or use the built-in ktest database?">
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39 <option value="builtinDB">Use built-in db</option>
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40 <option value="myownDB">Use a db from my history</option>
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41 </param>
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42 <when value="builtinDB">
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43 <param name="builtinDatabases" type="select" label="Select a built-in kraken database">
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44 <options from_data_table="krakenDBs">
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45 <filter type="sort_by" column="2" />
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46 <validator type="no_options" message="No databases are available" />
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47 </options>
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48 </param>
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49 </when>
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50 <when value="myownDB">
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51 <param name="myownDB" type="data" format="fasta" metadata_name="dbkey" label="Select database" />
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52 </when>
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53 </conditional>
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54
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55 <conditional name="quickMode">
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56 <param name="useQuickMode" type="select" label="Use Quick operation? (use first hit or hits)">
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57 <option value="useQuick">Use Quick operation</option>
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58 <option value="dontUseQuick">Do not use Quick operation</option>
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59 </param>
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60 <when value="useQuick">
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61 <param name="minHits" type="integer" label="Minimum number of hits required for classification (default:1)" value="1" default="1" />
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62 </when>
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63 </conditional>
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64
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65 <!-- <conditional name="libraryType">
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66 <param name="libtype" type="select" label="Is this library single- or paired-end?">
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67 <option value="single">Single-end</option>
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68 <option value="paired">Paired-end</option>
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69 </param>
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70 <when value="single">
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71 <param name="input1" type="data" format="fasta,fastq,fasta.gz,fasta.bz2,fa.gz,fq.gz,fa,fq" label="Fasta/Fastq file" />
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72 </when>
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73 <when value="paired">
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74 <param name="input1" type="data" format="fasta,fastq,fasta.gz,fasta.bz2,fa.gz,fq.gz,fa,fq" label="Left Fasta/Fastq file" />
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75 <param name="input2" type="data" format="fasta,fastq,fasta.gz,fasta.bz2,fa.gz,fq.gz,fa,fq" label="Right Fasta/Fastq file" />
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76 </when>
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77 </conditional> -->
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78 <conditional name="dataFormat">
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79 <param name="inputFormat" type="select" label="Please select input file type and library type.">
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80 <option value="singleFastQ">Single-end FastQ</option>
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81 <option value="pairedFastQ">Paired-end FastQ</option>
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82 <option value="singleFastA">Single-end FastA</option>
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83 <option value="pairedFastA">Paired-end FastA</option>
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84 </param>
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85 <when value="singleFastQ">
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86 <param name="input1" type="data" format="fastq,fastqillumina,fastqsanger,fq" label="FastQ file" />
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87 </when>
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88 <when value="pairedFastQ">
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89 <param name="input1" type="data" format="fastq,fastqillumina,fastqsanger,fq" label="Forward/Left FastQ file" />
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90 <param name="input2" type="data" format="fastq,fastqillumina,fastqsanger,fq" label="Reverse/Right FastQ file" />
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91 </when>
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92 <when value="singleFastA">
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93 <param name="input1" type="data" format="fasta, fa" label="FastA file" />
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94 </when>
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95 <when value="pairedFastA">
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96 <param name="input1" type="data" format="fasta, fa" label="Forward/Left FASTA file" />
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97 <param name="input2" type="data" format="fasta, fa" label="Reverse/Right FASTA file" />
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98 </when>
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99 </conditional>
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100
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101
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102 </inputs>
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103 <outputs>
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104 <data format="tabular" name="kraken_summary_tsv" label="${tool.name} output summary of ${on_string}" />
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105 <!-- <data name="classified_seqs_fq" format_source="input1" label="${tool.name}-classified sequences from ${on_string}" />
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106 <data name="unclassified_seqs_fq" format_source="input1" label="${tool.name}-unclassified sequences from ${on_string}" /> -->
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107 </outputs>
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108
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109 <help>
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110 This tool wraps the kraken taxonomic sequence classifier.
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111 </help>
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112 </tool>
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