view macros.xml @ 0:0f01dc62c4f3 draft default tip

planemo upload for repository https://github.com/rdurnik/aoptk commit df42dbae2ad18cec86a3b927123fdc3f1c82287c

<macros>
    <token name="@TOOL_VERSION@">0.1.6</token>
    <token name="@VERSION_SUFFIX@">0</token>

    <xml name="requirements">
        <requirement type="package" version="@TOOL_VERSION@">aoptk</requirement>
        <credentials name="email_credentials" 
                     label="Your e-mail address" 
                     version="1.0"
                     description="E-mail is required to follow NCBI/PubMed guidelines.">
            <variable name="email" inject_as_env="EMAIL" optional="true"/>
          </credentials>
    </xml>

    <xml name="inputs">
        <param argument="--query" type="text" value="" label="Your search term" help="Type your search term as you would in PubMed/Europe PMC.">
            <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits">
                    <add value="_" />
                    <add value=" " />
                    <add value="&apos;" />
                    <add value="&quot;" />
                    <add value="(" />
                    <add value=")" />
                    <add value="*" />
                    <add value="[" />
                    <add value="]" />
                    <add value="-" />
                    <add value=":" />
                    <add value="/" />
                    <!-- Lowercase Greek letters -->
                    <add value="α" />
                    <add value="β" />
                    <add value="γ" />
                    <add value="δ" />
                    <add value="ε" />
                    <add value="ζ" />
                    <add value="η" />
                    <add value="θ" />
                    <add value="ι" />
                    <add value="κ" />
                    <add value="λ" />
                    <add value="μ" />
                    <add value="ν" />
                    <add value="ξ" />
                    <add value="ο" />
                    <add value="π" />
                    <add value="ρ" />
                    <add value="σ" />
                    <add value="τ" />
                    <add value="υ" />
                    <add value="φ" />
                    <add value="χ" />
                    <add value="ψ" />
                    <add value="ω" />
                    <!-- Uppercase Greek letters -->
                    <add value="Α" />
                    <add value="Β" />
                    <add value="Γ" />
                    <add value="Δ" />
                    <add value="Ε" />
                    <add value="Ζ" />
                    <add value="Η" />
                    <add value="Θ" />
                    <add value="Ι" />
                    <add value="Κ" />
                    <add value="Λ" />
                    <add value="Μ" />
                    <add value="Ν" />
                    <add value="Ξ" />
                    <add value="Ο" />
                    <add value="Π" />
                    <add value="Ρ" />
                    <add value="Σ" />
                    <add value="Τ" />
                    <add value="Υ" />
                    <add value="Φ" />
                    <add value="Χ" />
                    <add value="Ψ" />
                    <add value="Ω" />
                </valid>
            </sanitizer>
            <validator type="regex">[0-9a-zA-Z_ ()*'"[\]\[\]\-:.\[\]α-ωΑ-Ω]+</validator>
        </param>
        <param name="literature_database" type="select" label="Select which database to search." help="PubMed only accepts searches with up to 10 000 results. No limit for Europe PMC.">
            <option value="pubmed" selected="true">PubMed</option>
            <option value="europepmc">EuropePMC</option>
        </param>
    </xml>


<token name="@init_scores@">
from matchms.importing import load_from_msp, scores_from_json
from matchms import Scores
#if $scores.use_scores == "True"
scores = scores_from_json("$scores_in")
join_type = "$scores.join_type"
#else
scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
join_type = "left"
#end if
</token>

<token name="@init_logger@">
from matchms import set_matchms_logger_level
set_matchms_logger_level("WARNING")
</token>   
</macros>