comparison rbdock.xml @ 6:07fa39ed62c7 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"

5:e4b7d1507a75

<tool id="rdock_rbdock" name="rDock docking" version="0.1.3" profile="19.01">
    <description>- perform protein-ligand docking with rDock</description>
    <macros>
        <import>rdock_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
ln -s '$active_site' receptor.as &&
ln -s '$receptor' receptor.mol2 &&
ln -s $receptor_prm receptor.prm &&
#if $name == 'Y':
  sdmodify -f_REC '$ligands' > ligands.sdf &&
#else
  ln -s '$ligands' ligands.sdf &&
#end if

    ]]></command>

    <configfiles>
        <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
RECEPTOR_FILE receptor.mol2
RECEPTOR_FLEX 3.0
        </configfile>
    </configfiles>

    <inputs>
        <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>
        <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>
        <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/>
        <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>
        <conditional name="filter">
            <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter">
                <option value="filter">Show filter options</option>
                <option value="no_filter">No filtering</option>

        <test expect_failure="true" expect_exit_code="23">
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="broken_ligand.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="top" value="1"/>
            </conditional>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_names.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="top" value="1"/>
            </conditional>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_nonames.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="top" value="1"/>
            </conditional>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_nonames.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="no_filter"/>
            </conditional>
            <param name="name" value="true"/>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_names.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="1"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="score" value="10"/>
                <param name="nscore" value="1"/>

                <assert_contents>
                    <has_text text="Rbt.Current_Directory"/>
                     <has_n_lines n="352"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

6:07fa39ed62c7

<tool id="rdock_rbdock" name="rDock docking" version="0.1.4" profile="19.01">
    <description>- perform protein-ligand docking with rDock</description>
    <macros>
        <import>rdock_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
ln -s '$active_site' receptor.as &&
ln -s '$receptor' receptor.mol2 &&

#if $custom_rec.custom_rec_select == 'true':
    ## simple check that the receptor file name is correct
    grep -q 'RECEPTOR_FILE receptor.mol2' $custom_rec.prm_file || (echo "Error: a custom receptor.prm file must contain the line 'RECEPTOR_FILE receptor.mol2'" >&2 && exit 1) &&
    ln -s '$custom_rec.prm_file' receptor.prm &&
#else
    ln -s '$receptor_prm' receptor.prm &&
#end if

#if $name == 'Y':
  sdmodify -f_REC '$ligands' > ligands.sdf &&
#else
  ln -s '$ligands' ligands.sdf &&
#end if

    ]]></command>

    <configfiles>
        <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
RECEPTOR_FILE receptor.mol2
#if $custom_rec.custom_rec_select == 'false':
RECEPTOR_FLEX $custom_rec.flex
#end if
        </configfile>
    </configfiles>

    <inputs>
        <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>
        <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>
        <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/>
        <conditional name="custom_rec">
            <param name="custom_rec_select" type="select" label="Use a custom receptor.prm file?" help="Useful for more advanced use-cases, such as tethered docking.">
                <option value="true">Use custom receptor.prm file</option>
                <option value="false" selected="true">Use default options (no user upload required)</option>
            </param>
            <when value="true">
                <param type="data" name="prm_file" format="txt" label="Receptor prm file" help="Note the file must contain the line 'RECEPTOR_FILE receptor.mol2', else the tool will fail."/>
            </when>
            <when value="false">
                <param name="flex" type="float" value="3.0" min="0.0" label="Receptor flex" help="Value for RECEPTOR_FLEX (default 3)"/>
            </when>
        </conditional>

        <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>
        <conditional name="filter">
            <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter">
                <option value="filter">Show filter options</option>
                <option value="no_filter">No filtering</option>

        <test expect_failure="true" expect_exit_code="23">
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="broken_ligand.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="flex" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="top" value="1"/>
            </conditional>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_names.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="flex" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="top" value="1"/>
            </conditional>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_nonames.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="flex" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="top" value="1"/>
            </conditional>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_nonames.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="3"/>
            <param name="flex" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="no_filter"/>
            </conditional>
            <param name="name" value="true"/>

        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_names.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="num" value="1"/>
            <param name="flex" value="3"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="score" value="10"/>
                <param name="nscore" value="1"/>

                <assert_contents>
                    <has_text text="Rbt.Current_Directory"/>
                     <has_n_lines n="352"/>
                </assert_contents>
            </output>
        </test>
        <!-- test with custom receptor.prm -->
        <test>
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_names.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="custom_rec_select" value="true"/>
            <param name="prm_file" value="receptor.prm"/>
            <param name="num" value="1"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="filter"/>
                <param name="score" value="10"/>
                <param name="nscore" value="1"/>
            </conditional>
            <param name="name"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Rbt.Current_Directory"/>
                     <has_n_lines n="352"/>
                </assert_contents>
            </output>
        </test>
        <!-- test with custom but broken receptor.prm -->
        <test expect_failure="true" expect_exit_code="1">
            <param name="receptor" value="receptor.mol2"/>
            <param name="ligands" value="ligands_names.sdf"/>
            <param name="active_site" value="receptor.as"/>
            <param name="custom_rec_select" value="true"/>
            <param name="prm_file" value="wrong_receptor.prm"/>
            <param name="num" value="1"/>
            <param name="seed" value="3"/>
            <conditional name="filter">
                <param name="filter_select" value="no_filter"/>
            </conditional>
            <param name="name"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark