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1 <tool id="kraken_combine" name="kraken_combine">
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2 <description>extract unique and common sequences from two kraken runs</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.4">python</requirement>
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5 </requirements>
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6 <command interpreter="python">kraken_combine.py
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7 --in1="${dataFormat.input1}"
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8 --set1-output-left=${set1OutputLeft}
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9 --set2-output-left=${set2OutputLeft}
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10 --unclassified-output-left=${unclassifiedOutputLeft}
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11 --intersection-output-left=${intersectionOutputLeft}
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12 --kraken-results1="${classificationSet1}"
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13 --kraken-results2="${classificationSet2}"
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14
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15 #if $dataFormat.inputFormat == "pairedFASTQ" or $dataFormat.inputFormat == "pairedFASTA":
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16 --in2="${dataFormat.input2}"
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17 --set1-output-right=${set1OutputRight}
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18 --set2-output-right=${set2OutputRight}
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19 --unclassified-output-right=${unclassifiedOutputRight}
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20 --intersection-output-right=${intersectionOutputRight}
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21 #end if
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22
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23 #if $dataFormat.inputFormat == "singleFASTQ" or $dataFormat.inputFormat == "pairedFASTQ":
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24 --input-format="fq"
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25 #else:
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26 --input-format="fa"
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27 #end if
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28
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29
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30
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31 </command>
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32 <inputs>
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33 <param name="classificationSet1" type="data" format="tabular" label="Kraken classification output set1" />
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34 <param name="classificationSet2" type="data" format="tabular" label="Kraken classification output set2" />
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35
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36 <conditional name="dataFormat">
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37 <param name="inputFormat" type="select" label="Please select input file type and library type.">
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38 <option value="singleFASTQ">Single-end FASTQ</option>
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39 <option value="pairedFASTQ">Paired-end FASTQ</option>
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40 <option value="singleFASTA">Single-end FASTA</option>
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41 <option value="pairedFASTA">Paired-end FASTA</option>
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42 </param>
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43 <when value="singleFASTQ">
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44 <param name="input1" type="data" format="fastq,fq.gz,fq" label="FASTQ file" />
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45 </when>
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46 <when value="pairedFASTQ">
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47 <param name="input1" type="data" format="fastq,fq.gz,fq" label="Forward/Left FASTQ file" />
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48 <param name="input2" type="data" format="fastq,fq.gz,fq" label="Reverse/Right FASTQ file" />
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49 </when>
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50 <when value="singleFASTA">
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51 <param name="input1" type="data" format="fasta,fasta.gz,fasta.bz2,fa.gz" label="FASTA file" />
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52 </when>
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53 <when value="pairedFASTA">
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54 <param name="input1" type="data" format="fasta,fasta.gz,fasta.bz2,fa.gz" label="Forward/Left FASTA file" />
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55 <param name="input2" type="data" format="fasta,fasta.gz,fasta.bz2,fa.gz" label="Reverse/Right FASTA file" />
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56 </when>
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57 </conditional>
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58 </inputs>
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59
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60 <outputs>
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61 <data format="input1" name="set1OutputLeft" label="Taxonomy1-unique sequences (R1) of ${on_string}" />
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62 <data format="input1" name="set2OutputLeft" label="Taxonomy2-unique sequences (R1) of ${on_string}" />
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63 <data format="input1" name="intersectionOutputLeft" label="Common sequences (R1) of ${on_string}" />
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64 <data format="input1" name="unclassifiedOutputLeft" label="Unclassified sequences (R1) of ${on_string}" />
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65
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66 <data format="input2" name="set1OutputRight" label="Taxonomy1-unique sequences (R2) of ${on_string}">
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67 <filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
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68 </data>
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69 <data format="input2" name="set2OutputRight" label="Taxonomy2-unique sequences (R2) of ${on_string}">
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70 <filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
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71 </data>
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72 <data format="input2" name="intersectionOutputRight" label="Common sequences (R2) of ${on_string}">
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73 <filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
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74 </data>
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75 <data format="input2" name="unclassifiedOutputRight" label="Unclassified sequences (R2) of ${on_string}">
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76 <filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
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77 </data>
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78 </outputs>
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79
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80 <help>
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81 This tool compares the classification results on a dataset using two different kraken-databases.
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82 </help>
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83 </tool>
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