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annotate wgmlst_sequence.xml @ 2:4394da33d837 draft default tip

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planemo upload for repository https://github.com/bvalot/pyMLST commit 142042a3856f8886031cacaa4fb28743a1bcd540
author bvalot
date Wed, 15 Nov 2023 12:22:07 +0000
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1 <tool id="wgmlst_sequence_wrapper"
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2 name="Sequences of cg/wgMLST database"
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3 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
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4 <description></description>
1
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5 <macros>
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6 <import>macro.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12 <version_command>wgMLST -v</version_command>
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13 <command>
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14 wgMLST sequence
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15 #if str($genes)
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16 -f '${genes}'
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17 #end if
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18 #if $reference
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19 --reference
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20 #end if
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21 '${database}' > '${sequence}'
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22 #if $log
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23 2> '${logfile}'
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="database" type="data"
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28 format="sqlite"
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29 label="cg/wgMLST database"
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30 help="Sqlite format from cg/wgMLST database" />
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31 <param name="genes" type="data"
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32 format="txt"
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33 label="Genes list"
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34 help="File containing list of genes to extract" />
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35 <param name="reference" type="boolean" checked="false"
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36 label="Report the number of gene found for each strain" />
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37 <param name="log" type="boolean" checked="false"
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38 label="Write log file" />
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39 </inputs>
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40 <outputs>
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41 <data name="logfile" format="txt" label="Sequence of
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42 ${database.name}: log">
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43 <filter>log</filter>
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44 </data>
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45 <data name="sequence" format="fasta" label="Sequence of ${database.name}: fasta" />
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46 </outputs>
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47 <tests>
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48 <test expect_num_outputs="1">
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49 <param name="database" value="wgmlst_ecoli.db" />
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50 <param name="genes" value="wgmlst_ecoli.db.gene" />
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51 <param name="reference" value="true" />
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52 <output name="sequence" ftype="fasta" file="wgmlst_ecoli.db.sequence" />
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53 </test>
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54 </tests>
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55 <help>
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56 **What it does**
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57
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58 Extract sequences from a wgMLST DATABASE.
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59
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60 **Options**
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61
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62 -f, --file FILENAME File containing list of coregenes to extract
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63 (default:all coregenes).
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64 --reference Return sequence of the reference instead of
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65 strains allele
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66
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67 **License and citation**
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68
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69 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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70 </help>
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71 <citations>
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72 </citations>
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73 </tool>