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Added the profile2cami tool, a component of the TaxonKit suite. #6085

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merged 11 commits into from
Jul 26, 2024
Merged

Added the profile2cami tool, a component of the TaxonKit suite. #6085

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33a53eb
Added the profile2cami tool, a component of the TaxonKit suite.
Alby-Git Jun 14, 2024
461a8a7
Renamed shed.yml -> .shed.yml
Alby-Git Jun 14, 2024
3db4745
Shrinked delnodes.dmp 684kb -> 150kb
Alby-Git Jun 17, 2024
d15df70
Renamed test.loc -> ncbi_taxonomy.loc
Alby-Git Jun 17, 2024
49cc76e
Adjusted taxonkit, removed folder profile2cami, added suite in .shed.yml
Alby-Git Jun 24, 2024
bb7d131
Updated Taxonkit to version 0.17.0 - worked on issues.
Alby-Git Jul 6, 2024
ef148fa
Renamed taxonomy.loc -> taxonomy.loc.test
Alby-Git Jul 7, 2024
4a88efd
Adjusted test, adjusted loc.sample
Alby-Git Jul 8, 2024
c66c0ed
Try to fix linting error
Alby-Git Jul 8, 2024
71fc99f
Resolving linting error
Alby-Git Jul 9, 2024
079f9b4
Adjusted the output label.
Alby-Git Jul 26, 2024
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18 changes: 18 additions & 0 deletions tools/taxonkit/.shed.yml
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name: taxonkit
owner: iuc
description: Tools for metagenomic profiling and analysis
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Its not used for profiling and specific to NCBI TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit something like that I guess

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.
17 changes: 17 additions & 0 deletions tools/taxonkit/macros.xml
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<macros>
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Please add bio.tool xml: https://bio.tools/taxonkit

<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">taxonkit</requirement>
<yield/>
</requirements>
</xml>
<token name="@TOOL_VERSION@">0.16.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.05</token>
<xml name="citations">
<citations>
<citation type="doi">10.1016/j.jgg.2021.03.006</citation>
<yield/>
</citations>
</xml>
</macros>
111 changes: 111 additions & 0 deletions tools/taxonkit/taxonkit_profile2cami.xml
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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="requirements" />
<command detect_errors="exit_code">
<![CDATA[
taxonkit profile2cami
--data-dir '${taxonomy.fields.path}'
--abundance-field '${abundance_field}'
--taxid-field '${taxid_field}'
#if $percentage:
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See @bernt-matthias comment https://github.com/galaxyproject/tools-iuc/pull/6096/files/0f22502b798ad0481fd372e66c1cb26e31734ee8#r1647385458
Can you please use truevalue and remove the if for all such cases ?

-p
#end if
#if $recompute_abd:
-R
#end if
#if $keep_zero:
-0
#end if
#if $sample_id:
-s '${sample_id}'
#end if
#if $taxonomy_id:
-t '${taxonomy_id}'
#end if
--show-rank '${show_rank}'
${input_file}
> '${cami_output}'
]]>
</command>
<inputs>
<param name="input_file" type="data" format="txt" label="Input Profile File" help="Input the tab-delimited profile file with TaxId and abundance columns." />
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Suggested change
<param name="input_file" type="data" format="txt" label="Input Profile File" help="Input the tab-delimited profile file with TaxId and abundance columns." />
<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="To have actual human-readable taxon names in the standardised output">
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Suggested change
<param argument="--taxonomy" type="select" label="NCBI taxonomy" help="To have actual human-readable taxon names in the standardised output">
<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." />
<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." />
<param name="keep_zero" type="boolean" value="false" label="Keep Zero Abundances" help="Check to keep taxons with abundance of zero." />
<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="show_rank" type="text" value="superkingdom,phylum,class,order,family,genus,species,strain" label="Show Ranks" help="Specify the ranks to show in the result file." />
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Can you use a type="select" and multiple="true" param for this ´, like this one:

         <param name="show_rank" type="select" multiple="true" label="Show Ranks">
            <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>

Make all options

</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" />
<output name="cami_output" file="output1_basic_functionality.tsv" />
</test>

<!-- Test 2: Using percentage flag -->
<test expect_num_outputs="1">
<param name="input_file" value="abundance.tsv" ftype="tsv" />
<param name="percentage" value="true" />
<output name="cami_output" file="output2_percentage_flag.tsv" />
</test>

<!-- 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" />
<output name="cami_output" file="output3_recompute_abd.tsv" />
</test>

<!-- 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" />
<output name="cami_output" file="output4_all_param.tsv" />
</test>
</tests>
<help>
<![CDATA[
**What is Profile2CAMI**

Profile2CAMI is a tool for converting metagenomic profile tables to CAMI format.

**Inputs**
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All info that is given in the input parameters can be removed from the help


- A tab-delimited profile file with TaxId and abundance columns.

**Outputs**

- A CAMI formatted file.

**Parameters**

- Abundance Field Index: Field index of the abundance column in the input data.
- TaxId Field Index: Field index of the TaxId column in the input data.
- Abundance in Percentage: Check if the abundance values are in percentage.
- Recompute Abundance: Check to recompute abundance if some TaxIds are deleted in the current taxonomy version.
- Keep Zero Abundances: Check to keep taxons with abundance of zero.
- Sample ID: Optional sample ID to include in the result file.
- Taxonomy ID: Optional taxonomy ID to include in the result file.
- Show Ranks: Specify the ranks to show in the result file.

For more information, please refer to the tool's documentation.
]]>
</help>
<expand macro="citations" />
</tool>
4 changes: 4 additions & 0 deletions tools/taxonkit/test-data/abundance.tsv
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83333 0.2 merged to 562
83333 0.2 absord 562
561 0.5 no change
91347 0.1 deleted
1 change: 1 addition & 0 deletions tools/taxonkit/test-data/ncbi_taxonomy.loc
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test-db-tox Test Database ${__HERE__}/test-db
12 changes: 12 additions & 0 deletions tools/taxonkit/test-data/output1_basic_functionality.tsv
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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 99.999999999999986
1224 phylum 2|1224 Bacteria|Proteobacteria 99.999999999999986
1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 99.999999999999986
91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 99.999999999999986
543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 89.999999999999986
561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 89.999999999999986
562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 40.000000000000000
12 changes: 12 additions & 0 deletions tools/taxonkit/test-data/output2_percentage_flag.tsv
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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
12 changes: 12 additions & 0 deletions tools/taxonkit/test-data/output3_recompute_abd.tsv
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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 100.000000000000028
1224 phylum 2|1224 Bacteria|Proteobacteria 100.000000000000028
1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 100.000000000000028
91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 100.000000000000028
543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 90.000000000000028
561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 90.000000000000028
562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 40.000000000000007
12 changes: 12 additions & 0 deletions tools/taxonkit/test-data/output4_all_param.tsv
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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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