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annotate tools/mentalist_call/mentalist_call.xml @ 54:750c83ff09e5 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/mentalist_v0.2 commit 3fbb2cdd490b9d979155da462a62e19e0cb2b569
author dfornika
date Thu, 24 May 2018 16:58:09 -0400
parents 4cc93ead2f2d
children 30cddbcc549b
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750c83ff09e5 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/mentalist_v0.2 commit 3fbb2cdd490b9d979155da462a62e19e0cb2b569
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1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2">
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2 <requirements>
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3 <requirement type="package" version="0.2.2">mentalist</requirement>
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4 </requirements>
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5 <edam_operations>
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6 <edam_operation>operation_3840</edam_operation>
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7 </edam_operations>
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8 <command detect_errors="exit_code"><![CDATA[
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9 mentalist
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10 call
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11 -o '$output_file'
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12 --db '$kmer_db.fields.path'
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13 --mutation_threshold '$mutation_threshold'
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14 --kt '$kmer_threshold'
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15 $output_votes
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16 $output_special
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17 #if $input_type.sPaired == "paired":
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18 -1 $input_type.pInput1 -2 $input_type.pInput2
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19 #elif $input_type.sPaired == "collections":
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20 -1 $input_type.fastq_collection.forward -2 $input_type.fastq_collection.reverse
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21 #end if
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22 ]]></command>
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23 <inputs>
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24 <conditional name="input_type">
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25 <param name="sPaired" type="select" label="Single Pair or Collection">
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26 <option value="collections">Paired-end Collections</option>
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27 <option value="paired">Paired-end</option>
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28 </param>
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29 <when value="paired">
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30 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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31 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
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32 </when>
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33 <when value="collections">
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34 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
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35 </when>
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36 </conditional>
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37 <param name="kmer_db" type="select">
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38 <options from_data_table="mentalist_databases">
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39 <validator type="no_options" message="No MentaLiST databases are available" />
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40 </options>
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41 </param>
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42 <param name="mutation_threshold" type="integer" label="Mutation threshold"
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43 help="Maximum number of mutations when looking for novel alleles."
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44 value="6" min="1" max="25" />
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45 <param name="kmer_threshold" type="integer" label="Kmer threshold"
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46 help="Minimum number of times a kmer is seen to be considered present in the sample."
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47 value="10" min="1" max="25" />
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48 <param name="output_votes" type="boolean" label="Output votes"
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49 argument="--output_votes" truevalue="--output_votes" falsevalue=""
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50 help="Outputs the results for the original voting algorithm" />
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51 <param name="output_special" type="boolean" label="Output special"
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52 argument="--output_special" truevalue="--output_special" falsevalue=""
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53 help="Outputs a fasta file with the alleles from special cases such as incomplete coverage, novel and multiple alleles." />
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54 </inputs>
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55 <outputs>
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56 <data name="output_file" format="tabular" />
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57 <data name="coverage_file" format="tabular" />
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58 </outputs>
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59 <help><![CDATA[
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60 ]]></help>
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61 <citations>
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62 <citation type="doi">10.1101/172858</citation>
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63 <citation type="doi">10.1099/mgen.0.000146</citation>
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64 </citations>
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65 </tool>