Mercurial > repos > iuc > chewbbaca_extractcgmlst
comparison ExtractCgMLST.xml @ 0:ad1b30369cdd draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
| author | iuc |
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| date | Wed, 25 Sep 2024 14:12:35 +0000 |
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| -1:000000000000 | 0:ad1b30369cdd |
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| 1 <tool id="chewbbaca_extractcgmlst" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description>Determine the set of loci that constitute the core genome</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 chewBBACA.py ExtractCgMLST | |
| 9 --t $threshold | |
| 10 #if $genes2remove: | |
| 11 --r '$genes2remove' | |
| 12 #end if | |
| 13 #if $genomes2remove: | |
| 14 --g '$genomes2remove' | |
| 15 #end if | |
| 16 -i '$input_file' -o 'output' | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param argument="--input-file" type="data" label="Allelic Profiles" format="tabular"/> | |
| 20 <section name="advanced" title="Advanced options"> | |
| 21 <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/> | |
| 22 <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list."> | |
| 23 <validator type="regex">[ .0-9]+</validator> | |
| 24 </param> | |
| 25 <param argument="--genes2remove" type="data" format="tabular" label="List of genes to exclude from analysis" optional="true" help="the list of genes listed in the "paralogous_counts.tsv" file created by the AlleleCall process."/> | |
| 26 </section> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}"> | |
| 30 <discover_datasets pattern="__name_and_ext__" directory="output"/> | |
| 31 </collection> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="input_file" value="results_alleles.tsv"/> | |
| 36 <output_collection name="output_collection" type="list"> | |
| 37 <element name="missing_loci_stats"> | |
| 38 <assert_contents> | |
| 39 <has_text_matching expression="GCA_000007265"/> | |
| 40 </assert_contents> | |
| 41 </element> | |
| 42 <element name="presence_absence"> | |
| 43 <assert_contents> | |
| 44 <has_text_matching expression="GCA_000007265"/> | |
| 45 </assert_contents> | |
| 46 </element> | |
| 47 </output_collection> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help> | |
| 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. | |
| 52 | |
| 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. | |
| 54 | |
| 55 .. class:: infomark | |
| 56 | |
| 57 **Note** | |
| 58 | |
| 59 The user can define a **space-separated** list of values for --threshold | |
| 60 </help> | |
| 61 <expand macro="citations" /> | |
| 62 </tool> |