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annotate tools/mentalist_call/mentalist_call.xml @ 12:efef2ecf139e draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty
author dfornika
date Wed, 11 Oct 2017 16:47:16 -0400
parents 0f74aa0cfb68
children c3cef07b5132
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0f74aa0cfb68 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy
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1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.2">
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2 <requirements>
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3 <requirement type="package" version="0.1.2">mentalist</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 mentalist
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7 call
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8 -o '$output_file'
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9 -s '$sample_name'
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10 --db '$kmer_db.fields.path'
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11 #if $discard_threshold
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12 -t '$discard_threshold'
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13 #end if
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14 $input_fastqs.forward $input_fastqs.reverse
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15 ]]></command>
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16 <inputs>
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17 <param name="sample_name" type="text"
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18 label="Sample Name" help="Sample Name" />
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19 <param name="kmer_db" type="select">
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20 <options from_data_table="mentalist_databases">
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21 <validator type="no_options" message="No MentaLiST databases are available" />
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22 </options>
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23 </param>
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24 <param name="discard_threshold" type="float"
0f74aa0cfb68 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy
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25 label="Discard Threshold" help="A read of length L is discarded if it has at less than (L - k) * t hits to the same locus in the kmer database, where k is the kmer length. 0 &lt;= t &lt;= 1"
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26 value="0.3" min="0" max="1" />
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27 <param name="skip_length" type="integer"
0f74aa0cfb68 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy
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28 label="Skip Length" help="Skip length between consecutive k-mers."
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29 value="1" min="1" max="32" />
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30 <param name="input_fastqs" type="data_collection" collection_type="paired" format="fastq"
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31 label="Input FastQ" help="FastQ input files" />
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32 </inputs>
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33 <outputs>
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34 <data name="output_file" format="tsv"/>
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35 </outputs>
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36 <help><![CDATA[
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37 ]]></help>
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38 <citations>
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39 <citation type="doi">10.1101/172858</citation>
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40 </citations>
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41 </tool>