annotate rxn_smarts_filter.xml @ 0:ce27129127e0 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"

<tool id="ctb_im_rxn_smarts_filter" name="Reaction SMARTS filter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using RDKit</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        rxn_smarts_filter
            -i '$infile'
            -if sdf
            $multi
            --meta
            -of sdf
            -o 'outp' &>> $logfile &&
        cat 'outp_metrics.txt' &>> $logfile &&
        gzip -d outp.sdf.gz
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
        <param name="multi" type="boolean" label="Multi mode" truevalue="--multi" falsevalue="" help="Output one file for each reaction"/>
    </inputs>
    <outputs>
        <data name="outfile" format="sdf" label="SDF output for ${tool.name}" from_work_dir="outp.sdf"/>
        <data name="logfile" format="txt" label="Logfile for ${tool.name}"/>
        <collection name="output_list" type="list">
            <filter>multi</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sdf$" ext="sdf" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <param name="multi" value="" />
            <output name="outfile" ftype="sdf">
                <assert_contents>
                    <has_line line="   -5.0090    3.0685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0"/>
                    <has_line line="OB(O)c1nc(N2CCOCC2)c2oc3ncccc3c2n1"/>
                    <has_line line="CO[C@@H]1[C@H](NC(=O)c2ccccc2)C[C@H]2O[C@]1(C)n1c3ccccc3c3c4c(c5c6ccccc6n2c5c31)C(=O)NC4"/>
                    <has_text_matching expression="^([^\$]+?\$\$\$\$){36}?$"/>
                </assert_contents>
            </output>
            <output name="logfile">
                <assert_contents>
                    <has_text text="Matched 36 molecules from a total of 36"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <param name="multi" value="--multi" />
            <output name="outfile" ftype="sdf">
                <assert_contents>
                    <has_line line="   -5.0090    3.0685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0"/>
                    <has_line line="OB(O)c1nc(N2CCOCC2)c2oc3ncccc3c2n1"/>
                    <has_line line="CO[C@@H]1[C@H](NC(=O)c2ccccc2)C[C@H]2O[C@]1(C)n1c3ccccc3c3c4c(c5c6ccccc6n2c5c31)C(=O)NC4"/>
                    <has_text_matching expression="^([^\$]+?\$\$\$\$){36}?$"/>
                </assert_contents>
            </output>
            <output name="logfile">
                <assert_contents>
                    <has_text text="Matched 36 molecules from a total of 36"/>
                </assert_contents>
            </output>

            <output_collection name="output_list" type="list">
                <element name="Sonogashira" ftype="sdf" >
                    <assert_contents>
                        <has_text text="COCCOc1cc2ncnc(Nc3cccc(C#C)c3)c2cc1OCCOC"/>
                        <has_text_matching expression="^([^\$]+?\$\$\$\$){1}?$"/>
                    </assert_contents>
                </element>
            </output_collection>

        </test>
    </tests>
    <help><![CDATA[
        ABCCDEFGHIJKLMNOPQRSTUVWXYZ
    ]]></help>
    <expand macro="citations" />
</tool>