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1 <tool id="serotypefinder" name="serotypefinder" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
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2 <requirements>
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3 <requirement type="package">serotypefinder</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6
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7 #if $reads.reads_select == 'collection'
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8 #set $name = $reads.coll.name.replace(' ', '_')
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9 #set $forward = $reads.coll.forward
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10 #set $reverse = $reads.coll.reverse
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11 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
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12 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
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13 gunzip -c $reverse > reverse.fastq;
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14 #set $reverse = './reverse.fastq'
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15 gunzip -c $forward > forward.fastq;
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16 #set $forward = './forward.fastq'
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17 #end if
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18 ln -s $forward ${name}_1.fastq;
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19 ln -s $reverse ${name}_2.fastq;
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20 #else
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21 #set $name = $reads.assembly.name.replace(' ', '_')
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22 #set $ga = $reads.assembly
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23 #set $infile = $name + ".fasta"
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24 ln -s $ga ${name}.fasta;
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25 #end if
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26 serotypefinder -x -i $infile
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27
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28 ]]></command>
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29 <inputs>
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30 <conditional name="reads">
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31 <param name="reads_select" type="select" label="Genome assembly or paired-end collection">
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32 <option value="collection">Paired collection from your history</option>
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33 <option value="genome">Genome Assembly</option>
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34 </param>
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35 <when value="collection">
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36 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
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37 </when>
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38 <when value="genome">
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39 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
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40 </when>
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data name="results" format="tabular" from_work_dir="results_tab.tsv" />
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45 </outputs>
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46 <help><![CDATA[
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47 Serotype predictions for E.coli.
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48 ]]></help>
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49 <citations>
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50 <citation type="bibtex">
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51 @misc{fleming,
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52 title={serotypefinder - Serotype Prediction for E. coli},
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53 journal={epub}, publisher={epub},
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54 author={Scheutz, Flemming},
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55 year={2023}, month={Max},
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56 url={https://bitbucket.org/genomicepidemiology/serotypefinder/src/master}},
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57
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58 </citation>
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59 </citations>
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60 </tool>
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