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annotate wgmlst_sequence.xml @ 0:a3cc35af3635 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author bvalot
date Thu, 16 Jun 2022 12:32:28 +0000
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a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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1 <tool id="wgmlst_sequence_wrapper" name="Sequences of cg/wgMLST database" version="2.1.3">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.1.3">pymlst</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <version_command>wgMLST -v</version_command>
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10 <command>
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11 wgMLST sequence
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12 #if str($genes)
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13 -f '${genes}'
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14 #end if
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15 #if $reference
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16 --reference
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17 #end if
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18 '${database}' > '${sequence}'
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19 #if $log
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20 2> '${logfile}'
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21 #end if
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22 </command>
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23 <inputs>
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24 <param name="database" type="data"
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25 format="sqlite"
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26 label="cg/wgMLST database"
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27 help="Sqlite format from cg/wgMLST database" />
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28 <param name="genes" type="data"
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29 format="txt"
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30 label="Genes list"
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31 help="File containing list of genes to extract" />
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32 <param name="reference" type="boolean" checked="false"
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33 label="Report the number of gene found for each strain" />
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34 <param name="log" type="boolean" checked="false"
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35 label="Write log file" />
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36 </inputs>
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37 <outputs>
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38 <data name="logfile" format="txt" label="Sequence of
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39 ${database.name}: log">
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40 <filter>log</filter>
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41 </data>
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42 <data name="sequence" format="fasta" label="Sequence of ${database.name}: fasta" />
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43 </outputs>
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44 <tests>
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45 <test expect_num_outputs="1">
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46 <param name="database" value="wgmlst_ecoli.db" />
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47 <param name="genes" value="wgmlst_ecoli.db.gene" />
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48 <param name="reference" value="true" />
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49 <output name="sequence" ftype="fasta" file="wgmlst_ecoli.db.sequence" />
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50 </test>
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51 </tests>
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52 <help>
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53 **What it does**
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54
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55 Extract sequences from a wgMLST DATABASE.
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56
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57 **Options**
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58
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59 -f, --file FILENAME File containing list of coregenes to extract
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60 (default:all coregenes).
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61 --reference Return sequence of the reference instead of
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62 strains allele
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63
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64 **License and citation**
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65
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66 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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67 </help>
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68 <citations>
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69 </citations>
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70 </tool>