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1 <tool id="most" name="MOST">
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2 <description>Determine MLST from sequencing reads</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.7.10">python</requirement>
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6 <requirement type="package" version="3.2.3">lxml</requirement>
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7 <requirement type="package" version="3.11">pyyaml</requirement>
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8 <requirement type="package" version="1.9">numpy</requirement>
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9 <requirement type="package" version="1.66">biopython</requirement>
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10 <requirement type="package" version="2.1.0">bowtie2</requirement>
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11 <requirement type="package" version="0.1.18">samtools</requirement>
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12 <requirement type="package" version="5.0.0">emboss</requirement>
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13 <requirement type="package" version="2.2.27">blast+</requirement>
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14 <requirement type="package" version="1.0">phemost</requirement>
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15 </requirements>
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16
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17 <command interpreter="bash">
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18 MOST.sh
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19 $fwd_file
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20 $rev_file
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21 $out1
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22 $out2
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23 "${organism.fields.file_path}"
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24 </command>
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25
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26 <inputs>
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27 <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/>
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28 <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/>
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29 <param name="organism" type="select" label="Select an organism">
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30 <options from_data_table="mlst_data">
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31 <column name="value" index="0"/>
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32 <column name="dbkey" index="1"/>
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33 <column name="name" index="2"/>
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34 <column name="time_stamp" index="3"/>
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35 <column name="file_path" index="4"/>
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36 <validator type="no_options" message="No indexes are available" />
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37 </options>
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38 </param>
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39 </inputs>
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40
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41 <outputs>
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42 <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/>
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43 <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/>
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44 </outputs>
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45
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46 <help>
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47 https://github.com/phe-bioinformatics/MOST
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48 </help>
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49 </tool>
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