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author nml
date Wed, 15 Mar 2017 13:56:48 -0400
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
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3 <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">sect</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command><![CDATA[
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12
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13 cp "$db" db.fasta &&
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14 #if $single_or_paired.type == "single"
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15 ln "$input_se" read.fastq &&
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16 kat sect 'db.fasta'
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17 read.fastq
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18 #elif $single_or_paired.type == "paired"
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19 ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
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20 kat sect 'db.fasta'
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21 read_1.fastq read_2.fastq
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22 #else
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23 ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
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24 kat sect 'db.fasta'
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25 read_1.fastq read_2.fastq
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26 #end if
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27
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28 @THREADS@
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30 --mer_len $kmer
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31
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32
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33 $keep_counts
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34
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35 -o results
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36
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37 ]]></command>
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38 <inputs>
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39 <expand macro="macro_input" />
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40
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41 <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
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42 <expand macro="macro_kmers" />
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43 <param name="keep_counts" type="boolean" falsevalue='--no_count_stats' truevalue='' checked='False' label="Fasta Count File" help="Produce a fasta style representation of the input sequence file containing K-mer coverage counts mapped across each sequence"/>
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44 </inputs>
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45 <outputs>
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46 <data format="tabular" name="stats" label='Stats' from_work_dir="results-stats.tsv" />
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47 <data format="txt" name="counts" label='Counts' from_work_dir="results-counts.cvg">
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48 <filter>keep_counts</filter>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input_se" value="input.fastq" />
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54 <param name="db" value="db.fasta" />
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55 <param name="keep_counts" value="False" />
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56 <output file="kat-sect-stats.tsv" name="stats" />
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57 </test>
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58 <test>
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59 <param name="input_se" value="input.fastq" />
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60 <param name="db" value="db.fasta" />
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61 <param name="keep_counts" value="True" />
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62 <output file="kat-sect-stats.tsv" name="stats" />
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63 <output file="kat-sect-counts.cvg" name="counts" />
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 https://kat.readthedocs.io/en/latest/using.html#sect
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68 ]]>
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70 </help>
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71 <expand macro="citations" />
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72 </tool>