comparison natural_product_likeness_calculator.xml @ 18:da45aa9141cf

ChemicalToolBoX update.

17:2f5a2e537ad6

<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.2">
    <description>likeness calculator</description>
    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,outfragments"></parallelism>
    <requirements>
        <requirement type="package" version="2.0">np-likeness-scorer</requirement>
    </requirements>
    <command>
        java -jar \$NPLS_JAR_PATH/NP-Likeness-2.0.jar
            -in "${infile}"
            -out "${outfile}"
            #if $reconstruct_fragments:
                -reconstructFragments true
                -outFragments $outfragments
            #end if
    </command>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param format="smi,sdf" name="infile" type="data" label="Molecule file" help="Dataset missing? See TIP below"/>
        <param name='reconstruct_fragments' type='boolean' label='Fragments-scores are written out in SMILES format' truevalue='' falsevalue='' />
    </inputs>
    <outputs>
        <data format="sdf" name="outfile" />
        <data format="tabular" name="outfragments">
            <filter>reconstruct_fragments is True</filter>
        </data>
    </outputs>
    <tests>

18:da45aa9141cf

<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.2.1">
    <description>likeness calculator</description>
    <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,outfragments"></parallelism>-->
    <requirements>
        <requirement type="package" version="2.0">np-likeness-scorer</requirement>
    </requirements>
    <command>
        ## NPLC is really picky with file extensions. We need to specify every datatype as file extension
        ## A workaround is to create a symlink with a proper file-extension.
        #import tempfile
        #set $temp_file = tempfile.NamedTemporaryFile()
        #set $temp_link = "%s.%s" % ($temp_file.name, $infile.ext)
        $temp_file.close()
        ln -s $infile $temp_link;

        java -jar \$NPLS_JAR_PATH/NP-Likeness-2.0.jar
            -in "${temp_link}"
            -out "${outfile}"
            #if $reconstruct_fragments:
                -reconstructFragments true
                -outFragments $outfragments
            #end if
        ;
        rm $temp_link
    </command>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param format="smi,sdf" name="infile" type="data" label="Molecule file" help="Dataset missing? See TIP below"/>
        <param name='reconstruct_fragments' type='boolean' label='Fragments-scores are written out in SMILES format' truevalue='' falsevalue='' />
    </inputs>
    <outputs>
        <data format_source="infile" name="outfile" />
        <data format="tabular" name="outfragments">
            <filter>reconstruct_fragments is True</filter>
        </data>
    </outputs>
    <tests>