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1 <tool id="kat_sect" name="KAT Sect" version="1.3.0">
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2 <description> SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.1">kat</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10
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11 ln "$db" db.fasta &&
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12 #if $single_or_paired.type == "single"
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13 ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq &&
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14 kat sect 'db.fasta'
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15 "$single_or_paired.input_se.element_identifier".fastq
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16 #elif $single_or_paired.type == "paired"
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17 ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
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18 kat sect 'db.fasta'
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19 "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq
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20 #else
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21 ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
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22 kat sect 'db.fasta'
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23 "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq
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24 #end if
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25 --threads \${GALAXY_SLOTS:-4}
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26 -o reads
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27
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28 ]]></command>
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29 <inputs>
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30 <conditional name="single_or_paired">
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31 <param name="type" type="select" label="Read type">
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32 <option value="single">Single-end</option>
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33 <option value="paired">Paired-end</option>
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34 <option value="collection">Collection Paired-end</option>
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35 </param>
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36 <when value="single">
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37 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
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38 </when>
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39 <when value="paired">
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40 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
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41 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
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42 </when>
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43 <when value="collection">
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44 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
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45 </when>
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46 </conditional>
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47 <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
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48 </inputs>
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49 <outputs>
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50 <data format="tabular" name="reads" label='Reads' from_work_dir="reads-stats.tsv" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="input" value="input.fastq" />
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55 <param name="db" value="db.fasta" />
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56 <output file="matched.fastq" ftype="fastqsanger" name="reads" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 http://kat.readthedocs.io/en/latest/using.html#filtering-tools
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61 ]]>
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62
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63 </help>
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64 <citations>
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65 </citations>
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66 </tool>
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