comparison rmsd_clustering.xml @ 2:b9c46dbe9605 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"

1:b001ebc8bf58

<tool id="biomd_rmsd_clustering" name="Hierarchical clustering" version="0.@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>from MD RMSD matrix data</description>
    <macros>
        <token name="@TOOL_VERSION@">1.5.2</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
        <requirement type="package" version="1.19.1">numpy</requirement>
        <requirement type="package" version="3.3.1">matplotlib</requirement>

                --heatmap '$hmap'
                --cmap '$cmap'
            #end if
            --start '$start'
            --end '$end'
            '$normalize'
]]></command>
    <inputs>
        <param label="JSON or tabular input file" type="data" format="json,tabular" name="inp" argument="--json"/>
        <param label="First trajectory frame to calculate distance matrix" value="0" type="integer" name="start" argument="--start"/>
        <param label="Last trajectory frame to calculate distance matrix" value="-1" type="integer" name="end" argument="--end"/>

            <output name="outp_mat" value="outp_mat.tabular"/>
            <output name="dend" value="dendrogram.png"/>
            <output name="hmap" value="heatmap.png"/>
            <output name="Z" value="Z.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

2:b9c46dbe9605

<tool id="biomd_rmsd_clustering" name="Hierarchical clustering" version="0.@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>from MD RMSD matrix data</description>
    <macros>
        <token name="@TOOL_VERSION@">1.5.2</token>
        <token name="@GALAXY_VERSION@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
        <requirement type="package" version="1.19.1">numpy</requirement>
        <requirement type="package" version="3.3.1">matplotlib</requirement>

                --heatmap '$hmap'
                --cmap '$cmap'
            #end if
            --start '$start'
            --end '$end'
            $normalize
]]></command>
    <inputs>
        <param label="JSON or tabular input file" type="data" format="json,tabular" name="inp" argument="--json"/>
        <param label="First trajectory frame to calculate distance matrix" value="0" type="integer" name="start" argument="--start"/>
        <param label="Last trajectory frame to calculate distance matrix" value="-1" type="integer" name="end" argument="--end"/>

            <output name="outp_mat" value="outp_mat.tabular"/>
            <output name="dend" value="dendrogram.png"/>
            <output name="hmap" value="heatmap.png"/>
            <output name="Z" value="Z.tabular"/>
        </test>
        <test expect_num_outputs="2">
            <param name="inp" value="inp.json"/>
            <param name="dendrogram" value="false"/>
            <param name="heatmap" value="false"/>
            <param name="clustering_method" value="average"/>
            <param name="cmap" value="plasma"/>
            <param name="start" value="0"/>
            <param name="end" value="-1"/>
            <param name="normalize" value="false"/>
            <output name="outp_mat" value="outp_mat_unnormalized.tabular"/>
            <output name="Z" value="Z_unnormalized.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**