annotate macros.xml @ 0:bd267e082f86 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon/ commit bb37578aa61bf4a47af262e02baf0a1c1d9d02c6

<macros>
    <token name="@TOOL_VERSION@">1.0.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@LICENSE@">GPL-2.0-or-later</token>
    <xml name="requirements">
        <requirements>
            <container type="docker">sebimer/samba-v4-qiime2:2024.2</container>
        </requirements>
    </xml>
    <xml name="numb_blanks_arg">
        <param argument="--numb_blanks" type="integer" label="Number of blank samples" value="1" min="0" help="Specifies the number of blanks included in the data set"/>
    </xml>
    <xml name="numb_ind_arg">
        <param argument="--numb_ind" type="text" label="Number of individuals per group" optional="false" help="A comma-separated vector (e.g. 3,2) indicating the number of individual samples in each group">
            <validator type="regex" message="Enter a comma-separated list of positive integers (e.g., 3,2)">^\d+(,\d+)*$</validator>
        </param>
    </xml>
    <xml name="runs_and_regression_args">
        <param argument="--runs" type="integer" label="Number of runs" value="2" min="1" max="10" help="Specifies the number of times that the function should run the decontamination procedure on the data."/>
        <param argument="--regression" type="integer" label="Regression" value="0" min="0" max="2" help="Specifies the regression equation used to calculate the constant. 0 = it chooses between regression 1 and regression 2 based on the lower threshold and upper threshold arguments. 1 = it always uses regression 1. 2 = it always uses regression 2"/>
        <param argument="--low_threshold" type="integer" label="Lower threshold" value="40" min="0" help="Selects the lower point for switching between regression 1 and regression 2. It is usually best not to change this value"/>
        <param argument="--up_threshold" type="integer" label="Upper threshold" value="400" min="0" help="Selects the higher point for switching between regression 1 and regression 2. It is usually best not to change this value"/>
    </xml>
    <xml name="thresh_args">
        <param argument="--thresh" type="float" label="Zero proportion threshold" value="0.7" min="0" max="1" help="This is the threshold at which if that proportion of 0s are present for an OTU within a group, all samples will be set to 0 for that OTU for that group"/>
        <param argument="--prop_thresh" type="float" label="Proportional threshold" value="0.00005" min="0" max="1" help="This is the threshold at which if the number of reads for a particular OTU are below this proportion, the OTU will be set to zero for all individuals in that group"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1002/edn3.11</citation>
        </citations>
    </xml>
    <xml name="creators">
        <creator>
            <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053"/>
        </creator>
    </xml>
</macros>