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annotate tools/mentalist_call/mentalist_call.xml @ 0:1d9e3950ce61 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
author dfornika
date Wed, 20 Dec 2017 17:36:03 -0500
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1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
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1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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2 <requirements>
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3 <requirement type="package" version="0.1.3">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 '$output_file'
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9 --db '$kmer_db.fields.path'
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10 #if $input_type.sPaired == "paired":
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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11 -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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12 #elif $input_type.sPaired == "collections":
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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13 -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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14 #end if
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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15 ]]></command>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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16 <inputs>
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17 <conditional name="input_type">
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18 <param name="sPaired" type="select" label="Single Pair or Collection">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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19 <option value="collections">Paired-end Collections</option>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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20 <option value="paired">Paired-end</option>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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21 </param>
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22 <when value="paired">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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23 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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24 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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25 </when>
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26 <when value="collections">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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27 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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28 </when>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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29 </conditional>
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30 <param name="kmer_db" type="select">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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31 <options from_data_table="mentalist_databases">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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32 <validator type="no_options" message="No MentaLiST databases are available" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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33 </options>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data name="output_file" format="tabular"/>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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38 </outputs>
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39 <help><![CDATA[
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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40 ]]></help>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
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41 <citations>
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42 <citation type="doi">10.1101/172858</citation>
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43 </citations>
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44 </tool>