view hamronize_tool.xml @ 4:cbfa52c8f1ef draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6

<tool id="hamronize_tool" name="hAMRonize" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Antimicrobial Resistance Analysis Reports into a common data structure</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
#import re

#set $no_origin_info_tools = ['mykrobe', 'tbprofiler']
#set $origin_tools = ['abricate', 'amrfinderplus', 'fargene', 'srst2', 'staramr']
#set $in_fname_tools = ['amrfinderplus', 'amrplusplus', 'ariba', 'csstar', 'deeparg', 'fargene', 'groot', 'kmerresistance', 'pointfinder', 'resfarms', 'rgi', 'srax', 'srst2']
#set $ref_db_name_tools = ['ariba', 'csstar', 'groot', 'srax']
#set $input_file_name = re.sub('[^\s\w\-\.]', '_', str($input.report.element_identifier))

hamronize 
    '$input.tool'
    '$input.report'
    --format '$format'
    --output '$output'
#if $input.tool not in $no_origin_info_tools
    #if $input.tool in $origin_tools and $input.origin.origin
        #if $input.origin.origin
    --analysis_software_version '$input.report.tool_version'
        #else
    --analysis_software_version '$input.origin.analysis_software_version'
        #end if
    --reference_database_version '$input.reference_database_version'
    #else
    --analysis_software_version '$input.analysis_software_version'
    --reference_database_version '$input.reference_database_version'
    #end if
#end if
#if $input.tool in $in_fname_tools
    #if str($input.input_file_name) != ''
    --input_file_name '$input.input_file_name'
    #else
    --input_file_name '$input_file_name'
    #end if
#end if
#if $input.tool in $ref_db_name_tools
    --reference_database_name '$input.reference_database_name'
#end if
    ]]>    </command>
    <inputs>
        <conditional name="input">
            <param name="tool" type="select" label="Tool">
                <option value="abricate" selected="true">ABRicate</option>
                <option value="amrfinderplus">AMRFinderPlus</option>
                <option value="amrplusplus">AMRplusplus</option>
                <option value="ariba">ARIBA</option>
                <option value="csstar">c-SSTAR</option>
                <option value="deeparg">DeepARG</option>
                <option value="fargene">fARGene</option>
                <option value="groot">GROOT</option>
                <option value="kmerresistance">KmerResistance</option>
                <option value="mykrobe">Mykrobe</option>
                <option value="pointfinder">PointFinder</option>
                <option value="resfams">ResFams</option>
                <option value="resfinder">ResFinder</option>
                <option value="rgi">RGI</option>
                <option value="srax">SraX</option>
                <option value="srst2">SRST2</option>
                <option value="staramr">StarAMR</option>
                <option value="tbprofiler">TBProfiler</option>
            </param>
            <when value="abricate">
                <expand macro="report" format="tabular" label="ABRicate Report file"/>
                <expand macro="origin" software="ABRicate"/>
            </when>
            <when value="amrfinderplus">
                <expand macro="report" format="tabular" label="AMRFinderPlus Report file"/>
                <expand macro="input_file_name"/>
                <expand macro="origin" software="AMRFinderPlus"/>
            </when>
            <when value="amrplusplus">
                <expand macro="report" format="tabular" label="AMRplusplus gene report"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="AMRplusplus"/>
                <expand macro="reference_database_version"/>
            </when>
            <when value="ariba">
                <expand macro="report" format="tabular" label="ARIBA output"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="ARIBA"/>
                <expand macro="reference_database_version"/>
                <expand macro="reference_database_name" software="ARIBA"/>
            </when>
            <when value="csstar">
                <expand macro="report" format="tabular" label="c-SSTAR output"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="c-SSTAR" />
                <expand macro="reference_database_version"/>
                <expand macro="reference_database_name" software="c-SSTAR"/>
            </when>
            <when value="deeparg">
                <expand macro="report" format="tabular" label="DeepARG output"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="DeepARG"/>
            </when>
            <when value="fargene">
                <expand macro="report" format="txt" label="fARGene HMM Search Result"/>
                <expand macro="input_file_name"/>
                <expand macro="origin" software="fARGene"/>
            </when>
            <when value="groot">
                <expand macro="report" format="tabular" label="GROOT output"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="GROOT" />
                <expand macro="reference_database_version"/>
                <expand macro="reference_database_name" software="GROOT"/>
            </when>
            <when value="kmerresistance">
                <expand macro="report" format="tabular" label="KmerResistance gene report"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="KmerResistance"/>
                <expand macro="reference_database_version"/>
            </when>
            <when value="mykrobe">
                <expand macro="report" format="json" label="Mykrobe Report file"/>
            </when>
            <when value="pointfinder">
                <param name="report" type="data" format="txt" label="PointFinder results"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="PointFinder"/>
                <expand macro="reference_database_version"/>
            </when>
            <when value="resfams">
                <param name="report" type="data" format="txt" label="ResFams results"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="ResFams"/>
                <expand macro="reference_database_version"/>
            </when>
            <when value="resfinder">
                <param name="report" type="data" format="tabular" label="ResFinder results"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="ResFinder"/>
                <expand macro="reference_database_version"/>
            </when>
            <when value="rgi">
                <param name="report" type="data" format="txt" label="RGI output"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="RGI"/>
                <expand macro="reference_database_version"/>
            </when>
            <when value="srax">
                <param name="report" type="data" format="tabular" label="SraX detected ARGs"/>
                <expand macro="input_file_name"/>
                <expand macro="analysis_software_version" software="SraX"/>
                <expand macro="reference_database_version"/>
                <expand macro="reference_database_name" software="SraX"/>
            </when>
            <when value="srst2">
                <expand macro="report" format="tabular" label="SRST2 report"/>
                <expand macro="input_file_name"/>
                <expand macro="origin" software="SRST2"/>
            </when>
            <when value="staramr">
                <expand macro="report" format="tabular" label="StarAMR ResFinder output"/>
                <expand macro="origin" software="StarAMR"/>
            </when>
            <when value="tbprofiler">
                <param name="report" type="data" format="tabular" label="TBProfiler output"/>
            </when>
        </conditional>
        <param argument="--format" type="select" label="Output format">
            <option value="tsv" selected="True">Tabular</option>
            <option value="json">JSON</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string} (${input.tool})">
            <change_format>
                <when input="format" value="json" format="json"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <!-- abricate -->
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="tool" value="abricate" />
                <param name="report" value="abricate/report.tsv" ftype="tabular" />
                <conditional name="origin">
                    <param name="origin" value="false"/>
                    <param name="analysis_software_version" value="tool_v_1"/>
                </conditional>
                <param name="reference_database_version" value="db_v_1"/>
            </conditional>
            <param name="format" value="tsv" />
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="8"/>
                    <has_n_columns n="36"/>
                    <has_text text="input_file_name"/>
                    <has_text text="GCF_010120755.1_ASM1012075v1_genomic"/>
                    <has_text text="vanS-M"/>
                    <has_text text="db_v_1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="tool" value="abricate" />
                <param name="report" value="abricate/report.tsv" ftype="tabular" />
                <conditional name="origin">
                    <param name="origin" value="false"/>
                    <param name="analysis_software_version" value="tool_v_1"/>
                </conditional>
                <param name="reference_database_version" value="db_v_1"/>
            </conditional>
            <param name="format" value="json" />
            <output name="output" ftype="json">
                <assert_contents>
                    <has_text text="input_file_name"/>
                    <has_text text="GCF_010120755.1_ASM1012075v1_genomic"/>
                    <has_text text="vanS-M"/>
                    <has_text text="db_v_1"/>
                </assert_contents>
            </output>
        </test>
        <!-- ariba -->
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="tool" value="ariba" />
                <param name="report" value="ariba/report.tsv" ftype="tabular" />
                <param name="input_file_name" value="ariba_report" />
                <param name="analysis_software_version" value="ariba_v1" />
                <param name="reference_database_version" value="db_v_1" />
                <param name="reference_database_name" value="dbname" />
            </conditional>
            <param name="format" value="tsv" />
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="257"/>
                    <has_n_columns n="36"/>
                    <has_text text="input_file_name"/>
                    <has_text text="ariba_report"/>
                    <has_text text="AAC_3__IId"/>
                    <has_text text="ariba_v1"/>
                    <has_text text="db_v_1"/>
                    <has_text text="dbname"/>
                </assert_contents>
            </output>
        </test>
        <!-- mykrobe -->
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="tool" value="mykrobe" />
                <param name="report" value="mykrobe/mykrobe.json" ftype="json" />
            </conditional>
            <param name="format" value="tsv" />
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_n_columns n="36"/>
                    <has_text text="input_file_name"/>
                    <has_text text="rpoB"/>
                    <has_text text="v0.10.0"/>
                    <has_text text="NC_000962.3"/>
                    <has_text text="mykrobe"/>
                </assert_contents>
            </output>
        </test>
        <!-- rgi -->
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="tool" value="rgi" />
                <param name="report" value="rgi/rgi.txt" ftype="txt" />
                <param name="analysis_software_version" value="rgi_v1" />
                <param name="reference_database_version" value="card_v1" />
            </conditional>
            <param name="format" value="tsv" />
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="42"/>
                    <has_n_columns n="36"/>
                    <has_text text="input_file_name"/>
                    <has_text text="rgi.txt"/>
                    <has_text text="oqxA"/>
                    <has_text text="CARD"/>
                    <has_text text="card_v1"/>
                    <has_text text="rgi_v1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

hAMRonization parses multiple Antimicrobial Resistance Analysis Reports 
from disparate antimicrobial resistance gene detection tools into a single 
unified format.

This is an implementation of the hAMRonization AMR detection specification 
scheme which supports gene presence/absence resistance and mutational resistance 
(if supported by the underlying tool).

**Inputs**

Report or output of an antimicrobial resistance gene detection tool:

* abricate: abricate's output report i.e., OUTPUT.tsv
* amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
* ariba: ariba's output report i.e., OUTDIR/OUTPUT.tsv
* rgi: rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
* resfinder: resfinder's output report i.e., data_resfinder.json
* resfinder4: resfinder4's tabular output report i.e., ResFinder_results_tab.txt
* srax: srax's output report i.e., sraX_detected_ARGs.tsv
* deeparg: deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
* kmerresistance: kmerresistance's output report i.e., OUTPUT.KmerRes
* srst2: srst2's output report i.e., OUTPUT_srst2_report.tsv
* staramr: staramr's output report i.e., resfinder.tsv
* csstar: csstar's output report i.e., OUTPUT.tsv
* amrplusplus: amrplusplus's output report i.e., gene.tsv
* resfams: resfams's output report i.e., resfams.tblout
* groot: groot's output report i.e., OUTPUT.tsv (from `groot report`)

More: https://github.com/pha4ge/hAMRonization/#usage

]]></help>
    <expand macro="citations"/>
</tool>