comparison sucos_max.xml @ 5:d4c67ced6abc draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"

4:85fad59f8168

<tool id="sucos_max_score" name="Max SuCOS score" version="0.2.2">
    <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
    <macros>
        <import>sucos_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/sucos_max.py'
            -i '$input'
            -o '$output'
        #for $cluster in $clusters
            '$cluster'
        #end for
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
        <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." />
    </inputs>
    <outputs>
        <data format="sdf" name="output" label="The scored ligands"/>
    </outputs>
    <tests>

            <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="Max_SuCOS_Score" />
                    <has_text text="Cum_SuCOS_Score" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

**Input**

The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.

.. class:: infomark

**Output**

The same SD file as the input ligands with  the following properties added:

5:d4c67ced6abc

<tool id="sucos_max_score" name="Max SuCOS score" version="0.2.3">
    <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
    <macros>
        <import>sucos_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/sucos_max.py'
            -i '$input'
            -o '$output'
        #if $filter_field and $filter_value
            --filter-field '$filter_field' --filter-value $filter_value
        #end if
        #for $cluster in $clusters
            '$cluster'
        #end for
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
        <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." />
        <param name="filter_field" type="text" label="Filter field" optional="true"
               help="Filter output using this field's values. (e.g. Max_SuCOS_Score or Cum_SuCOS_Score)">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
                <mapping initial="none"/>
            </sanitizer>
        </param>
        <param name="filter_value" type="float" label="Filter value" optional="true"
               help="Filter out scores less than this value."/>
    </inputs>
    <outputs>
        <data format="sdf" name="output" label="The scored ligands"/>
    </outputs>
    <tests>

            <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="Max_SuCOS_Score" />
                    <has_text text="Cum_SuCOS_Score" />
                    <has_n_lines n="2224" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
            <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
            <param name="filter_field" value="Cum_SuCOS_Score"/>
            <param name="filter_value" value="15"/>
            <output name="output" ftype="sdf">
                <assert_contents>
                    <has_text text="Max_SuCOS_Score" />
                    <has_text text="Cum_SuCOS_Score" />
                    <has_n_lines n="686" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

**Input**

The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.

Optional filtering of the output is possible, for instance to retain only records with SuCOS scores greater that a
certain value. Use the optional 'Filter field' and 'Filter value' parameters. The 'Filter field' would typically
be one of the properties listed below.

.. class:: infomark

**Output**

The same SD file as the input ligands with  the following properties added: