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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <!-- <requirement type="binary">@BINARY@</requirement> -->
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5 <requirement type="package" version="1.1">khmer</requirement>
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6 </requirements>
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7 <version_command>@BINARY@ --version</version_command>
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8 </xml>
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9 <token name="TABLEPARAMS">#if $parameters.type == "simple"
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10 --ksize=20
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11 --n_tables=4
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12 --min-tablesize=$parameters.tablesize
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13 #else
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14 --ksize=$parameters.ksize
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15 --n_tables=$parameters.n_tables
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16 --min-tablesize=$parameters.tablesize_specific
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17 #end if</token>
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18 <xml name="tableinputs">
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19 <conditional name="parameters">
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20 <param name="type"
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21 type="select"
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22 label="Advanced Parameters"
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23 help="ksize, n_hashess, a specific hashsize" >
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24 <option value="simple"
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25 selected="true">
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26 Hide
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27 </option>
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28 <option value="specific">
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29 Show
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30 </option>
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31 </param>
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32 <when value="simple">
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33 <param name="hashsize"
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34 type="select"
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35 label="Sample Type"
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36 display="radio">
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37 <option value="1e9"
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38 selected="true">
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39 Microbial Genome
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40 </option>
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41 <option value="2e9">
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42 Animal Transcriptome
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43 </option>
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44 <option value="4e9">
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45 Small Animal Genome or Low-Diversity Metagenome
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46 </option>
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47 <option value="16e9">
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48 Large Animal Genome
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49 </option>
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50 </param>
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51 </when>
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52 <when value="specific">
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53 <param name="ksize"
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54 type="integer"
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55 value="20"
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56 label="ksize"
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57 help="k-mer size to use" />
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58 <param name="n_hashes"
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59 type="integer"
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60 min="1"
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61 value="4"
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62 label="n_hashes"
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63 help="number of hash tables to use" />
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64 <param name="hashsize_specifc"
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65 type="text"
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66 label="hashsize"
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67 help="lower bound on the hashsize to use" />
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68 </when>
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69 </conditional>
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70 </xml>
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71 <xml name="input_sequence_filename">
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72 <param name="input_sequence_filename"
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73 type="data"
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74 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
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75 label="FAST[AQ] file(s)" />
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76 </xml>
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77 <xml name="input_counting_table_filename">
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78 <param name="input_counting_table_filename"
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79 type="data"
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80 label="the k-mer counting table to query"
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81 help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer counting table." />
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82 </xml>
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83 <xml name="abundance-histogram-output">
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84 <data name="output_histogram_filename"
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85 format="text"
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86 label="${tool.name} k-mer abundance histogram. The
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87 columns are: (1) k-mer abundance, (2) k-mer count, (3)
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88 cumulative count, (4) fraction of total distinct
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89 k-mers.">
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90 </data>
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91 </xml>
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92 </macros>
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