comparison nested_collection.xml @ 2:7a0951d0e13e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038

1:86770eea5b09

<tool id="batched_set_list_creator" name="Create nested list" version="3.0.1">
    <description>based on filenames and batch sizes</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>python $__tool_directory__/nested_collection.py

        </repeat>
        <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
    </inputs>
    <outputs>
        <collection name="batched_fractions" type="list:list" label="Pooled batched data">
          <discover_datasets pattern="[a-zA-z0-9_]*___(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.mzid" ext="mzid" visible="true" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="batchsize" value="2"/>

                    <element name="fraction_three_spectra" value="empty_file3.mzid"/>
                    <element name="fraction_four_spectra" value="empty_file4.mzid"/>
                </collection>
            </param>
            <output_collection name="batched_fractions" type="list:list">
                <element name="batch0">
                    <element name="inputfn0" file="empty_file1.mzid"/>
                    <element name="inputfn1" file="empty_file2.mzid"/>
                </element>
                <element name="batch1">
                    <element name="inputfn0" file="empty_file3.mzid"/>
                    <element name="inputfn1" file="empty_file4.mzid"/>
                </element>
            </output_collection>
        </test>

                    <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
                    <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
                </collection>
            </param>
            <output_collection name="batched_fractions" type="list:list">
                <element name="batch0">
                    <element name="inputfn0" file="empty_file1.mzid"/>
                    <element name="inputfn1" file="empty_file2.mzid"/>
                    <element name="inputfn2" file="empty_file3.mzid"/>
                </element>
                <element name="batch1">
                    <element name="inputfn0" file="empty_file4.mzid"/>
                    <element name="inputfn1" file="empty_file5.mzid"/>
                    <element name="inputfn2" file="empty_file6.mzid"/>
                </element>
            </output_collection>

                    <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
                    <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
                </collection>
            </param>
            <output_collection name="batched_fractions" type="list:list">
                <element name="batch0">
                    <element name="inputfn0" file="empty_file1.mzid"/>
                    <element name="inputfn1" file="empty_file2.mzid"/>
                </element>
                <element name="batch1">
                    <element name="inputfn0" file="empty_file3.mzid"/>
                </element>
                <element name="batch2">
                    <element name="inputfn0" file="empty_file4.mzid"/>
                    <element name="inputfn1" file="empty_file5.mzid"/>
                </element>
                <element name="batch3">
                    <element name="inputfn0" file="empty_file6.mzid"/>
                </element>
            </output_collection>
        </test>
    </tests>

2:7a0951d0e13e

<tool id="batched_set_list_creator" name="Create nested list" version="3.1">
    <description>based on filenames and batch sizes</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>python $__tool_directory__/nested_collection.py

        </repeat>
        <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
    </inputs>
    <outputs>
        <collection name="batched_fractions" type="list:list" label="Pooled batched data">
          <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.mzid" ext="mzid" visible="true" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="batchsize" value="2"/>

                    <element name="fraction_three_spectra" value="empty_file3.mzid"/>
                    <element name="fraction_four_spectra" value="empty_file4.mzid"/>
                </collection>
            </param>
            <output_collection name="batched_fractions" type="list:list">
                <element name="pool0_batch0">
                    <element name="inputfn0" file="empty_file1.mzid"/>
                    <element name="inputfn1" file="empty_file2.mzid"/>
                </element>
                <element name="pool0_batch1">
                    <element name="inputfn0" file="empty_file3.mzid"/>
                    <element name="inputfn1" file="empty_file4.mzid"/>
                </element>
            </output_collection>
        </test>

                    <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
                    <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
                </collection>
            </param>
            <output_collection name="batched_fractions" type="list:list">
                <element name="set1_batch0">
                    <element name="inputfn0" file="empty_file1.mzid"/>
                    <element name="inputfn1" file="empty_file2.mzid"/>
                    <element name="inputfn2" file="empty_file3.mzid"/>
                </element>
                <element name="set2_batch1">
                    <element name="inputfn0" file="empty_file4.mzid"/>
                    <element name="inputfn1" file="empty_file5.mzid"/>
                    <element name="inputfn2" file="empty_file6.mzid"/>
                </element>
            </output_collection>

                    <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
                    <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
                </collection>
            </param>
            <output_collection name="batched_fractions" type="list:list">
                <element name="set1_batch0">
                    <element name="inputfn0" file="empty_file1.mzid"/>
                    <element name="inputfn1" file="empty_file2.mzid"/>
                </element>
                <element name="set1_batch1">
                    <element name="inputfn0" file="empty_file3.mzid"/>
                </element>
                <element name="set2_batch2">
                    <element name="inputfn0" file="empty_file4.mzid"/>
                    <element name="inputfn1" file="empty_file5.mzid"/>
                </element>
                <element name="set2_batch3">
                    <element name="inputfn0" file="empty_file6.mzid"/>
                </element>
            </output_collection>
        </test>
    </tests>