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annotate wgmlst_msa.xml @ 1:5b2c48fa0175 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
author bvalot
date Wed, 07 Dec 2022 15:25:06 +0000
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1 <tool id="wgmlst_msa_wrapper" name="MSA of cg/wgMLST database"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
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3 <description></description>
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4 <macros>
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5 <import>macro.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <stdio>
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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11 <version_command>wgMLST -v</version_command>
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12 <command>
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13 wgMLST msa
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14 #if str($genes)
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15 -f '${genes}'
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16 #end if
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17 #if $realign
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18 --realign
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19 #end if
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20 '${database}' > '${msa}'
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21 #if $log
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22 2> '${logfile}'
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23 #end if
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24 </command>
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25 <inputs>
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26 <param name="database" type="data"
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27 format="sqlite"
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28 label="cg/wgMLST database"
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29 help="Sqlite format from cg/wgMLST database" />
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30 <param name="genes" type="data"
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31 format="txt"
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32 label="Genes list"
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33 help="File containing list of genes to extract" />
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34 <param name="realign" type="boolean" checked="false"
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35 label="Realign genes with same length" />
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36 <param name="log" type="boolean" checked="false"
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37 label="Write log file" />
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38 </inputs>
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39 <outputs>
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40 <data name="logfile" format="txt" label="Sequence of
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41 ${database.name}: log">
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42 <filter>log</filter>
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43 </data>
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44 <data name="msa" format="fasta" label="MSA of ${database.name}: fasta" />
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45 </outputs>
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46 <tests>
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47 <test expect_num_outputs="1">
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48 <param name="database" value="wgmlst_ecoli.db" />
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49 <param name="genes" value="wgmlst_ecoli.db.gene" />
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50 <param name="realign" value="true" />
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51 <output name="msa" ftype="fasta" file="wgmlst_ecoli.db.msa" />
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52 </test>
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53 </tests>
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54 <help>
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55 **What it does**
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56
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57 Compute Multiple Sequence Alignment from a wgMLST DATABASE
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58
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59 **Options**
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60
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61 -f, --file FILENAME File containing list of coregenes to extract
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62 (default:all coregenes).
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63 -r, --realign Realign genes with same length (Default:No).
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64
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65 **License and citation**
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66
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67 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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68 </help>
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69 <citations>
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70 </citations>
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71 </tool>