comparison scoary.xml @ 1:77d50ec2bcf2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit 43a8ab018d2f2ab7827cfe62a8dbcf202e368e83

0:42a1a5750539

<tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>calculates the assocations between all genes in the accessory genome and the traits</description>
    <macros>
        <token name="@TOOL_VERSION@">1.6.16</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">scoary</requirement>
    </requirements>
    <version_command>scoary --version</version_command>
    <command detect_errors="exit_code"><![CDATA[

                    <option value="P">Empirical p-value from permutations</option>
                </param>
            </repeat>
            <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" />
            <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" />
            <param name="collapse" argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>
            <param name="input_newicktree" optional="true" argument="-n" type="data" format="newick" label="Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally." />
        </section>

        <!-- Output Options -->
        <section name="output_options" title="Output Options" expanded="true">

1:77d50ec2bcf2

<tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>calculates the assocations between all genes in the accessory genome and the traits</description>
    <macros>
        <token name="@TOOL_VERSION@">1.6.16</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">scoary</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">scoary</requirement>
    </requirements>
    <version_command>scoary --version</version_command>
    <command detect_errors="exit_code"><![CDATA[

                    <option value="P">Empirical p-value from permutations</option>
                </param>
            </repeat>
            <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" />
            <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" />
            <param argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>
            <param name="input_newicktree" optional="true" argument="-n" type="data" format="newick" label="Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally." />
        </section>

        <!-- Output Options -->
        <section name="output_options" title="Output Options" expanded="true">