comparison macros.xml @ 2:c1751dfb4d94 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"

1:d605800d956c

		</citations>
	</xml>
	<xml name="requirements">
		<requirements>
			<requirement type="package" version="@VERSION@">transit</requirement>
			<yield />
		</requirements>
	</xml>
	<token name="@VERSION@">2.5.2</token>
	<xml name="outputs">
        <yield />
        <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
    </xml>
    <xml name="replicates">

    </xml>
    <xml name="ignore_tas">
        <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
        <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
    </xml>
    <xml name="standard_inputs">
    	<expand macro="inputs" />
    	<yield />
    	<expand macro="ignore_tas" />
    </xml>
    <token name="@LINK_INPUTS@">
        <![CDATA[
            #if str($mode.replicates) == 'Batch':
                #set $input_files = $mode.inputs

        ]]>
    </token>
    <token name="@STANDARD_OPTIONS@">
        -iN $nterm
        -tC $cterm
    </token>
</macros>

2:c1751dfb4d94

		</citations>
	</xml>
	<xml name="requirements">
		<requirements>
			<requirement type="package" version="@VERSION@">transit</requirement>
            <requirement type="package" version="3.7">python</requirement>
			<yield />
		</requirements>
	</xml>
	<token name="@VERSION@">3.0.1</token>
	<xml name="outputs">
        <yield />
        <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
    </xml>
    <xml name="replicates">

    </xml>
    <xml name="ignore_tas">
        <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
        <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
    </xml>
    <xml name="normal">
        <param name="normalization" argument="-n" type="select" label="Normalization method"  value="TTR">
            <option value="TTR">TTR</option>
            <option value="nonorm">No Normalization</option>
            <option value="nzmean">Non-Zero Mean</option>
            <option value="totreads">Total read counts</option>
            <option value="zinfnb">Zero inflated Negative Binomial model</option>
            <option value="quantile">Quantile Normalization</option>
            <option value="betageom">Beta-Geometric Correction</option>
        </param>
    </xml>
    <xml name="standard_inputs">
    	<expand macro="inputs" />
    	<yield />
    	<expand macro="ignore_tas" />
    	<expand macro="normal" />
    </xml>
    <token name="@LINK_INPUTS@">
        <![CDATA[
            #if str($mode.replicates) == 'Batch':
                #set $input_files = $mode.inputs

        ]]>
    </token>
    <token name="@STANDARD_OPTIONS@">
        -iN $nterm
        -tC $cterm
        -n $normalization
    </token>
</macros>