comparison staramr_search.xml @ 16:4d83eccf5f81 draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84

15:be818ae858e4

<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
    <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
    <macros>
        <token name="@VERSION@">0.8.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">staramr</requirement>
	<!-- The staramr conda package includes the mlst software, but the list of schemes 
	     changes depending on the version. I specify the exact version here to make sure
             the list of schemes provided is consistent -->
	<requirement type="package" version="2.22.0">mlst</requirement>
    </requirements>
    <version_command>staramr --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re

    ]]></command>
    <inputs>
        <param type="data" name="genomes" format="fasta" multiple="true"/>
        <conditional name="pointfinder_db">
            <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
                <option value="disabled" selected="true">Disable PointFinder</option>
                <option value="salmonella">Salmonella</option>
                <option value="campylobacter">Campylobacter</option>
                <option value="custom">Unvalidated</option>
            </param>
	    <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism -->
	    <when value="disabled"/>
	    <when value="salmonella"/>
	    <when value="campylobacter"/>

	    <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->
            <when value="custom">
                <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results.">
                    <option value="enterococcus_faecalis">enterococcus_faecalis</option>
                    <option value="enterococcus_faecium">enterococcus_faecium</option>
                    <option value="escherichia_coli" selected="true">escherichia_coli</option>
                    <option value="helicobacter_pylori">helicobacter_pylori</option>
                    <option value="klebsiella">klebsiella</option>
                    <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option>
                    <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option>
                    <option value="plasmodium_falciparum">plasmodium_falciparum</option>
                    <option value="staphylococcus_aureus">staphylococcus_aureus</option>

                <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            </output_collection>
        </test>
        <test>
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            <param name="use_pointfinder" value="custom" />
            <param name="pointfinder_custom" value="escherichia_coli" />

            <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
            <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
            <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
            <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />

    </tests>
    <help><![CDATA[
staramr
=======

staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.

Usage
-----

1. Select your genome contigs (in FASTA format).

.. _staramr: https://github.com/phac-nml/staramr
.. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
.. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
.. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
.. _webservice: https://cge.food.dtu.dk/services/ResFinder/
    ]]></help>
    <citations>
        <citation type="bibtex">
            @Article{microorganisms10020292,
            	AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.},

16:4d83eccf5f81

<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
    <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
    <macros>
        <token name="@VERSION@">0.9.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">staramr</requirement>
	<!-- The staramr conda package includes the mlst software, but the list of schemes 
	     changes depending on the version. I specify the exact version here to make sure
             the list of schemes provided is consistent -->
	<requirement type="package" version="2.23.0">mlst</requirement>
    </requirements>
    <version_command>staramr --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re

    ]]></command>
    <inputs>
        <param type="data" name="genomes" format="fasta" multiple="true"/>
        <conditional name="pointfinder_db">
            <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
                <option value="disabled" selected="true">Disable PointFinder</option>                
                <option value="campylobacter">Campylobacter</option>
                <option value="enterococcus_faecalis">enterococcus_faecalis</option>
                <option value="enterococcus_faecium">enterococcus_faecium</option>
                <option value="escherichia_coli">escherichia_coli</option>      
                <option value="helicobacter_pylori">helicobacter_pylori</option>          
                <option value="salmonella">Salmonella</option>
                <option value="custom">Unvalidated</option>
            </param>
	    <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism -->
	    <when value="disabled"/>
        <when value="campylobacter"/>
        <when value="enterococcus_faecalis"/>
        <when value="enterococcus_faecium"/>
        <when value="escherichia_coli"/>
        <when value="helicobacter_pylori"/>
	    <when value="salmonella"/>

	    <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->
            <when value="custom">
                <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results.">                   
                    <option value="klebsiella">klebsiella</option>
                    <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option>
                    <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option>
                    <option value="plasmodium_falciparum">plasmodium_falciparum</option>
                    <option value="staphylococcus_aureus">staphylococcus_aureus</option>

                <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            </output_collection>
        </test>
        <test>
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            <param name="use_pointfinder" value="escherichia_coli" />

            <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
            <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
            <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
            <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />

    </tests>
    <help><![CDATA[
staramr
=======

staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by their respective webservices_) and compiles a summary report of detected antimicrobial resistance genes.

Usage
-----

1. Select your genome contigs (in FASTA format).

.. _staramr: https://github.com/phac-nml/staramr
.. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
.. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
.. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
.. _webservices: http://www.genomicepidemiology.org/services/
    ]]></help>
    <citations>
        <citation type="bibtex">
            @Article{microorganisms10020292,
            	AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.},