Added the profile2cami tool, a component of the TaxonKit suite. #6085
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| name: taxonkit | ||
| owner: iuc | ||
| description: TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit | ||
| homepage_url: https://bioinf.shenwei.me/taxonkit/ | ||
| long_description: | | ||
| TaxonKit is a set of tools for analyzing and manipulating taxonomic data. It includes utilities for converting metagenomic profile tables to CAMI format, among other functionalities. | ||
| remote_repository_url: https://github.com/shenwei356/taxonkit | ||
| categories: | ||
| - Metagenomics | ||
| type: unrestricted | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "Wrapper for TaxonKit function: {{ tool_name }}." | ||
| suite: | ||
| name: "suite_taxonkit" | ||
| description: "A suite of tools that brings the TaxonKit project into Galaxy." | ||
| long_description: | | ||
| TaxonKit is a set of tools for analyzing and manipulating taxonomic data, including converting metagenomic profile tables to CAMI format. |
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| <macros> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">taxonkit</requirement> | ||
| <yield/> | ||
| </requirements> | ||
| </xml> | ||
| <token name="@TOOL_VERSION@">0.17.0</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">21.05</token> | ||
| <xml name="biotools"> | ||
| <xrefs> | ||
| <xref type="bio.tools">taxonkit</xref> | ||
| </xrefs> | ||
| </xml> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1016/j.jgg.2021.03.006</citation> | ||
| <yield/> | ||
| </citations> | ||
| </xml> | ||
| </macros> | ||
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| <tool id="profile2cami" name="Profile2CAMI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>Convert metagenomic profile table to CAMI format</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="biotools"/> | ||
| <expand macro="requirements" /> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
| taxonkit profile2cami | ||
| --data-dir '${taxonomy.fields.path}' | ||
| --abundance-field '${abundance_field}' | ||
| --taxid-field '${taxid_field}' | ||
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| $percentage | ||
| $recompute_abd | ||
| $keep_zero | ||
| $no_sum_up | ||
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| #if $sample_id: | ||
| -s '${sample_id}' | ||
| #end if | ||
| #if $taxonomy_id: | ||
| -t '${taxonomy_id}' | ||
| #end if | ||
| --show-rank '${ranks}' | ||
|
There was a problem hiding this comment. can you put this in an if condition, so that if nothing is selected, all ranks are used as is the default by the tool ? also, please adjust the test for it, that's more convenient for the user |
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| ${input_file} | ||
| > '${cami_output}' | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="input_file" type="data" format="txt" label="Input Profile File" help="A tab-delimited profile file with TaxId and abundance columns." /> | ||
| <param argument="--taxonomy" type="select" label="NCBI taxonomy" help="This NCBI database is used to map human-readable taxon names to TaxId's."> | ||
| <options from_data_table="ncbi_taxonomy"> | ||
| <validator message="No NCBI database is available" type="no_options"/> | ||
| </options> | ||
| </param> | ||
| <param name="abundance_field" type="integer" value="2" label="Abundance Field Index" help="Field index of abundance in the input data." /> | ||
| <param name="taxid_field" type="integer" value="1" label="TaxId Field Index" help="Field index of TaxId in the input data." /> | ||
| <param name="percentage" type="boolean" value="false" label="Abundance in Percentage" help="Check if the abundance values are in percentage." truevalue="-p" falsevalue=""/> | ||
| <param name="recompute_abd" type="boolean" value="false" label="Recompute Abundance" help="Check to recompute abundance if some TaxIds are deleted in the current taxonomy version." truevalue="-R" falsevalue=""/> | ||
| <param name="keep_zero" type="boolean" value="false" label="Keep Zero Abundances" help="Check to keep taxons with abundance of zero." truevalue="-0" falsevalue=""/> | ||
| <param name="no_sum_up" type="boolean" value="false" label="Do Not Sum Up Abundance" help="Do not sum up abundance from child to parent TaxIds." truevalue="-S" falsevalue="" /> | ||
| <param name="sample_id" type="text" value="" label="Sample ID" help="Optional sample ID to include in the result file." /> | ||
| <param name="taxonomy_id" type="text" value="" label="Taxonomy ID" help="Optional taxonomy ID to include in the result file." /> | ||
| <param name ="ranks" argument="--show-rank" type="select" multiple="true" label="Show Ranks" help="Specify the ranks to show in the result file."> | ||
| <option value="superkingdom">Superkingdom</option> | ||
| <option value="phylum">Phylum</option> | ||
| <option value="class">Class</option> | ||
| <option value="order">Order</option> | ||
| <option value="family">Family</option> | ||
| <option value="genus">Genus</option> | ||
| <option value="species">Species</option> | ||
| <option value="strain">Strain</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="cami_output" format="tsv" label="Converted CAMI Output" /> | ||
| </outputs> | ||
| <tests> | ||
| <!-- Test 1: Basic functionality with default parameters --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
| <param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
| <output name="cami_output" file="output1_basic_functionality.tsv" /> | ||
| </test> | ||
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| <!-- Test 2: Using percentage flag --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
| <param name="percentage" value="true" /> | ||
| <param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
| <output name="cami_output" file="output2_percentage_flag.tsv" /> | ||
| </test> | ||
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| <!-- Test 3: Recomputing abundance with deleted TaxIds --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
| <param name="recompute_abd" value="true" /> | ||
| <param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
| <output name="cami_output" file="output3_recompute_abd.tsv" /> | ||
| </test> | ||
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| <!-- Test 4: Profile2Cami with all parameters checked --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
| <param name="percentage" value="true" /> | ||
| <param name="recompute_abd" value="true" /> | ||
| <param name="keep_zero" value="true" /> | ||
| <param name="no_sum_up" value="true" /> | ||
| <param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
| <output name="cami_output" file="output4_all_param.tsv" /> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <![CDATA[ | ||
| **What is Profile2CAMI** | ||
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| Profile2CAMI is a tool for converting metagenomic profile tables to CAMI format. | ||
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| **Inputs** | ||
|
There was a problem hiding this comment. All info that is given in the input parameters can be removed from the help |
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| - A tab-delimited profile file with TaxId and abundance columns. | ||
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| **Outputs** | ||
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| - A CAMI formatted file. | ||
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| For more information, please refer to the tool's documentation. | ||
| ]]> | ||
| </help> | ||
| <expand macro="citations" /> | ||
| </tool> | ||
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| 83333 0.2 merged to 562 | ||
| 83333 0.2 absord 562 | ||
| 561 0.5 no change | ||
| 91347 0.1 deleted |
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| test-db-tox Test Database ${__HERE__}/test-db |
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| @SampleID: | ||
| @Version:0.10.0 | ||
| @Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
| @TaxonomyID: | ||
| @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
| 2 superkingdom 2 Bacteria 100.000000000000000 | ||
| 1224 phylum 2|1224 Bacteria|Proteobacteria 100.000000000000000 | ||
| 1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 100.000000000000000 | ||
| 91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 100.000000000000000 | ||
| 543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 90.000000000000000 | ||
| 561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 90.000000000000000 | ||
| 562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 40.000000000000000 |
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| @SampleID: | ||
| @Version:0.10.0 | ||
| @Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
| @TaxonomyID: | ||
| @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
| 2 superkingdom 2 Bacteria 1.000000000000000 | ||
| 1224 phylum 2|1224 Bacteria|Proteobacteria 1.000000000000000 | ||
| 1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 1.000000000000000 | ||
| 91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 1.000000000000000 | ||
| 543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 0.900000000000000 | ||
| 561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 0.900000000000000 | ||
| 562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 0.400000000000000 |
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| @SampleID: | ||
| @Version:0.10.0 | ||
| @Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
| @TaxonomyID: | ||
| @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
| 2 superkingdom 2 Bacteria 190.000000000000000 | ||
| 1224 phylum 2|1224 Bacteria|Proteobacteria 190.000000000000000 | ||
| 1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 190.000000000000000 | ||
| 91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 190.000000000000000 | ||
| 543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 90.000000000000000 | ||
| 561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 90.000000000000000 | ||
| 562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 40.000000000000000 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,12 @@ | ||
| @SampleID: | ||
| @Version:0.10.0 | ||
| @Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
| @TaxonomyID: | ||
| @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
| 2 superkingdom 2 Bacteria 0.500000000000000 | ||
| 1224 phylum 2|1224 Bacteria|Proteobacteria 0.500000000000000 | ||
| 1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 0.500000000000000 | ||
| 91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 0.500000000000000 | ||
| 543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 0.500000000000000 | ||
| 561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 0.500000000000000 | ||
| 562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 0.400000000000000 |
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Please add bio.tool xml: https://bio.tools/taxonkit