Mercurial > repos > iuc > chewbbaca_extractcgmlst

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author iuc
date Wed, 25 Sep 2024 14:12:35 +0000
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1 <tool id="chewbbaca_extractcgmlst" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Determine the set of loci that constitute the core genome</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 chewBBACA.py ExtractCgMLST
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9 --t $threshold
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10 #if $genes2remove:
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11 --r '$genes2remove'
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12 #end if
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13 #if $genomes2remove:
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14 --g '$genomes2remove'
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15 #end if
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16 -i '$input_file' -o 'output'
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input-file" type="data" label="Allelic Profiles" format="tabular"/>
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20 <section name="advanced" title="Advanced options">
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21 <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
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22 <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list.">
ad1b30369cdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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23 <validator type="regex">[ .0-9]+</validator>
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24 </param>
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25 <param argument="--genes2remove" type="data" format="tabular" label="List of genes to exclude from analysis" optional="true" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process."/>
ad1b30369cdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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26 </section>
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27 </inputs>
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28 <outputs>
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29 <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}">
ad1b30369cdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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30 <discover_datasets pattern="__name_and_ext__" directory="output"/>
ad1b30369cdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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31 </collection>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input_file" value="results_alleles.tsv"/>
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36 <output_collection name="output_collection" type="list">
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37 <element name="missing_loci_stats">
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38 <assert_contents>
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39 <has_text_matching expression="GCA_000007265"/>
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40 </assert_contents>
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41 </element>
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42 <element name="presence_absence">
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43 <assert_contents>
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44 <has_text_matching expression="GCA_000007265"/>
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45 </assert_contents>
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46 </element>
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47 </output_collection>
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48 </test>
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49 </tests>
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50 <help>
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51 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
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52
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53 cgMLST schemas are defined as the set of loci that are present in all strains under analysis or, due to sequencing/assembly limitations, >95% of strains analyzed. In order to have a robust definition of a cgMLST schema for a given bacterial species, a set of representative strains of the diversity of a given species should be selected.
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54
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55 .. class:: infomark
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56
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57 **Note**
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58
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59 The user can define a **space-separated** list of values for --threshold
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60 </help>
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61 <expand macro="citations" />
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62 </tool>