comparison staramr_search.xml @ 4:1e8ec0f861ff draft

planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446

3:9047a1d3d8ea

<tool id="staramr_search" name="staramr" version="0.2.2">
    <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
    <requirements>
        <requirement type="package" version="0.2.2">staramr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re

        #set $named_genomes = ''

        --percent-length-overlap-pointfinder $advanced.plength_pointfinder

        $advanced.report_all_blast
        $advanced.exclude_negatives
        $advanced.exclude_resistance_phenotypes

        --output-summary $summary
        --output-resfinder $resfinder
        #if $use_pointfinder.enable
            --output-pointfinder $pointfinder

                   min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
            <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
                   help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
            <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
            <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
        <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />

            <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
            <param name="pid_threshold" value="99.8" />

            <output name="summary" file="test4-summary.tsv" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
staramr
=======

-----

1. Select your genome contigs (in FASTA format).
2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported).
3. Run the tool.

Output
------

There are 5 different output files produced by `staramr` as well as a collection of additional files.

4:1e8ec0f861ff

<tool id="staramr_search" name="staramr" version="0.3.0">
    <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
    <requirements>
        <requirement type="package" version="0.3.0">staramr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re

        #set $named_genomes = ''

        --percent-length-overlap-pointfinder $advanced.plength_pointfinder

        $advanced.report_all_blast
        $advanced.exclude_negatives
        $advanced.exclude_resistance_phenotypes

        #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
            --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
        #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
            --no-exclude-genes
        #end if

        --output-summary $summary
        --output-resfinder $resfinder
        #if $use_pointfinder.enable
            --output-pointfinder $pointfinder

                   min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
            <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
                   help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
            <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
            <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
            <conditional name="exclude_genes">
                <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
                    <option value="default" selected="true">Exclude default list of AMR genes</option>
                    <option value="custom">Provide a custom list of AMR genes to exclude</option>
                    <option value="none">Do not exclude any AMR genes</option>
                </param>
                <when value="default" />
                <when value="custom">
                    <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
                </when>
                <when value="none" />
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
        <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />

            <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
            <param name="pid_threshold" value="99.8" />

            <output name="summary" file="test4-summary.tsv" ftype="tabular" />
        </test>
        <test>
            <param name="genomes" value="test-aminoglycoside.fsa" />

            <output name="summary" file="test5-summary.tsv" ftype="tabular" />
        </test>
        <test>
            <param name="genomes" value="test-aminoglycoside.fsa" />
            <param name="exclude_genes_condition" value="none" />

            <output name="summary" file="test6-summary.tsv" ftype="tabular" />
        </test>
        <test>
            <param name="genomes" value="test-aminoglycoside.fsa" />
            <param name="exclude_genes_condition" value="custom" />
            <param name="exclude_genes_file" value="genes_to_exclude.tsv" />

            <output name="summary" file="test5-summary.tsv" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
staramr
=======

-----

1. Select your genome contigs (in FASTA format).
2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported).
3. Run the tool.

Input
-----

Genomes
```````

staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.

Exclude genes file
``````````````````

Setting **Provide a custom list of AMR genes to exclude** in the **Advanced options** allows you to pass a file containing a list of genes to exclude from the results. The file must start with a line **#gene_id** and the gene names must correspond to the sequence IDs in the ResFinder/PointFinder databases.  For example:

::

    #gene_id
    aac(6')-Iaa_1_NC_003197

Output
------

There are 5 different output files produced by `staramr` as well as a collection of additional files.