comparison align-it.xml @ 2:06d9381593a4 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit 00844534f9a2ffdf41fb9d5186d9a1e574c302d2"

1:10c0df29e6d1

<tool id="ctb_alignit" name="Pharmacophore alignment" version="1.0.3.1">
    <description>and optimization (Align-it)</description>
    <requirements>
        <requirement type="package" version="1.0.3">align_it</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
        align-it
            #if str($database.ext).strip() == 'phar':

            $scoreOnly
            $withExclusion
]]>
    </command>
    <inputs>
        <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/>
        <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference molecule"/>

        <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups to be used in the alignment">
            <option value='AROM' selected="true">aromatic rings</option>
            <option value='HDON' selected="true">hydrogen bond donors</option>
            <option value='HACC' selected="true">hydrogen bond acceptors</option>

            <option value='TVERSKY_DB'>TVERSKY_DB</option>
        </param>

    </inputs>
    <outputs>
        <data name="aligned_pharmacophores" format="txt" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
        <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
            <change_format>
                <when input="oformat" value="inchi" format="inchi"/>
                <when input="oformat" value="sdf" format="sdf"/>
            </change_format>

    <tests>
        <test>
            <param name="database" ftype="sdf" value="CID_2244.sdf"/>
            <param name="reference" ftype="sdf" value="CID_2244.sdf"/>
            <param name="oformat" value="sdf"/>
            <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" />
            <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" />
            <output name="score_result_file" file="aliginit_scores.tabular.tabular" />
        </test>
    </tests>
    <help>

2:06d9381593a4

<tool id="ctb_alignit" name="Pharmacophore alignment" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>and optimization (Align-it)</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.4</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">align_it</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
        align-it
            #if str($database.ext).strip() == 'phar':

            $scoreOnly
            $withExclusion
]]>
    </command>
    <inputs>
        <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/>
        <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference molecule"/>

        <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups to be used in the alignment">
            <option value='AROM' selected="true">aromatic rings</option>
            <option value='HDON' selected="true">hydrogen bond donors</option>
            <option value='HACC' selected="true">hydrogen bond acceptors</option>

            <option value='TVERSKY_DB'>TVERSKY_DB</option>
        </param>

    </inputs>
    <outputs>
        <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
        <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
            <change_format>
                <when input="oformat" value="inchi" format="inchi"/>
                <when input="oformat" value="sdf" format="sdf"/>
            </change_format>

    <tests>
        <test>
            <param name="database" ftype="sdf" value="CID_2244.sdf"/>
            <param name="reference" ftype="sdf" value="CID_2244.sdf"/>
            <param name="oformat" value="sdf"/>
            <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" ftype="phar" />
            <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" />
            <output name="score_result_file" file="aliginit_scores.tabular.tabular" />
        </test>
    </tests>
    <help>