comparison catWrapper.xml @ 8:5b2cc63d7a21 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets commit 424954037a50876b306f397efd8e9790f62416bd

7:55cf9d9defd1

<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1">
    <description>tail-to-head by specifying how</description>
    <command><![CDATA[
        #if $headers == 0:
            #set $concat_command = "cat"
        #else:
            #set $concat_command = 'tail -q -n +'+ str(int($headers)+1)

                <option value="simple_collections">2 Collections</option>
                <option value="paired_collection">Paired collection</option>
                <option value="nested_collection">Nested collection</option>
            </param>
            <when value="singles">
                <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/>
            </when>
            <when value="paired_collection">
                <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collection to concatenate"/>
                <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">
                    <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>
                    <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>
                    <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option>
                </param>

        </data>
        <data name="paired_out_file" label="${global_condition.inputs.element_identifier}" auto_format="true">
            <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter>
        </data>
        <collection name="paired_output" type="paired" label="Concatenation by strtand">
            <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" visible="false" directory="concatenated"/>
            <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
        </collection>
        <collection name="list_output" type="list" label="Concatenation by pairs">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" visible="false" directory="concatenated"/>
            <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter>
        </collection>
    </outputs>
    <tests>
        <!-- Single files concatenation -->
        <test> <!-- Test 2 single files concatenation with no other option -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1.bed,2.bed"/>
            <param name="dataset_names" value="No" />
            <param name="headers" value="0" />
            <output name="out_file1" file="cat_wrapper_out1.bed"/>
        </test>
        <test> <!-- Test 2 single files concatenation with dataset names activated -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1.bed,2.bed"/>
            <param name="dataset_names" value="Yes" />
            <param name="headers" value="0" />
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
        </test>
        <test> <!-- Test 2 single files concatenation skipping 1 line -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1.bed,2.bed"/>
            <param name="dataset_names" value="No" />
            <param name="headers" value="1" />
            <output name="out_file1" file="cat_wrapper_out3.bed"/>
        </test>
        <test> <!-- Test gz handling with no options -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
            <param name="dataset_names" value="No" />
            <param name="headers" value="0" />
            <output name="out_file1" file="1.fastq.gz" decompress="True"/>
        </test>
        <test> <!-- Test gz handling with options -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
            <param name="dataset_names" value="Yes" />
            <param name="headers" value="4" />
            <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>
        </test>
        <!-- Test paired options -->
        <test> <!-- Test paired collection concatenation by_pair with no other option -->
            <param name="input_type" value="paired_collection" />
            <param name="paired_cat_type" value="by_pair"/>
            <param name="inputs">
                <collection type="list:paired">
                    <element name="2">

                <element name="2" file="2.fastq"/>
                <element name="3" file="3.fastq"/>
                <element name="4" file="4.fastq"/>
            </output_collection>
        </test>
        <test> <!-- Test paired collection concatenation by_strand with no other option -->
            <param name="input_type" value="paired_collection" />
            <param name="paired_cat_type" value="by_strand"/>
            <param name="inputs">
                <collection type="list:paired">
                    <element name="2">

            <output_collection name="paired_output" type="paired" >
                <element name="forward" file="f.fastq"/>
                <element name="reverse" file="r.fastq"/>
            </output_collection>
        </test>
        <test> <!-- Test 2 collections concatenation -->
            <param name="input_type" value="simple_collections" />
            <param name="collection_cat_type" value="two_collections"/>
            <param name="input_1">
                <collection type="list">
                    <element name="2" value="2_f.fastq"/>
                    <element name="3" value="3_f.fastq"/>
                    <element name="4" value="4_f.fastq"/>

                <element name="2" file="2.fastq"/>
                <element name="3" file="3.fastq"/>
                <element name="4" file="4.fastq"/>
            </output_collection>
        </test>
        <test> <!-- Test 2 collections concatenation with other options-->
            <param name="input_type" value="simple_collections" />
            <param name="collection_cat_type" value="two_collections"/>
            <param name="input_1">
                <collection type="list">
                    <element name="1_f.fastq.gz" value="1_f.fastq.gz"/>
                </collection>
            </param>

            <param name="headers" value="4" />
            <output_collection name="list_output" type="list" count="1" >
                <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/>
            </output_collection>
        </test>
        <test> <!-- Test nested collections concatenation -->
            <param name="input_type" value="nested_collection" />
            <param name="inputs">
                <collection type="list:list">
                    <element name="2">
                        <collection type="list">

            <output_collection name="list_output" type="list" count="2" >
                <element name="2" file="2.fastq"/>
                <element name="3" file="3.fastq"/>
            </output_collection>
        </test>
        <test> <!-- Test nested collections concatenation with options and gzip-->
            <param name="input_type" value="nested_collection" />
            <param name="inputs">
                <collection type="list:list">
                    <element name="1">
                        <collection type="list">

-----

Adapted from galaxy's catWrapper.xml to allow multiple input files.

    </help>
</tool>

8:5b2cc63d7a21

<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.2">
    <description>tail-to-head while specifying how</description>
    <command><![CDATA[
        #if $headers == 0:
            #set $concat_command = "cat"
        #else:
            #set $concat_command = 'tail -q -n +'+ str(int($headers)+1)

                <option value="simple_collections">2 Collections</option>
                <option value="paired_collection">Paired collection</option>
                <option value="nested_collection">Nested collection</option>
            </param>
            <when value="singles">
                <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" format="fastq,fastq.gz,txt,tabular,bed"
                       help="All inputed datasets will be concatenated tail-to-head."/>
            </when>
            <when value="paired_collection">
                <param name="inputs" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,txt,tabular,bed"
                       label="Input paired collection to concatenate"/>
                <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">
                    <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>
                    <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>
                    <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option>
                </param>

        </data>
        <data name="paired_out_file" label="${global_condition.inputs.element_identifier}" auto_format="true">
            <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter>
        </data>
        <collection name="paired_output" type="paired" label="Concatenation by strtand">
            <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" format="fastq" visible="false" directory="concatenated"/>
            <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
        </collection>
        <collection name="list_output" type="list" label="Concatenation by pairs">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" format="fastq" visible="false" directory="concatenated"/>
            <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter>
        </collection>
    </outputs>
    <tests>
        <!-- Single files concatenation -->
        <test expect_num_outputs="1"> <!-- Test 1 single files concatenation with no other option -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1.bed,2.bed"/>
            <param name="dataset_names" value="No" />
            <param name="headers" value="0" />
            <output name="out_file1" file="cat_wrapper_out1.bed"/>
        </test>
        <test expect_num_outputs="1"> <!-- Test 2 single files concatenation with dataset names activated -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1.bed,2.bed"/>
            <param name="dataset_names" value="Yes" />
            <param name="headers" value="0" />
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
        </test>
        <test expect_num_outputs="1"> <!-- Test 3 single files concatenation skipping 1 line -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1.bed,2.bed"/>
            <param name="dataset_names" value="No" />
            <param name="headers" value="1" />
            <output name="out_file1" file="cat_wrapper_out3.bed"/>
        </test>
        <test expect_num_outputs="1"> <!-- Test 4 gz handling with no options -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
            <param name="dataset_names" value="No" />
            <param name="headers" value="0" />
            <output name="out_file1" file="1.fastq.gz" decompress="True"/>
        </test>
        <test expect_num_outputs="1"> <!-- Test 5 gz handling with options -->
            <param name="input_type" value="singles" />
            <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
            <param name="dataset_names" value="Yes" />
            <param name="headers" value="4" />
            <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>
        </test>
        <!-- Test paired options -->
        <test expect_num_outputs="1"> <!-- Test 6 paired collection concatenation by_pair with no other option -->
            <param name="input_type" value="paired_collection" />
            <param name="paired_cat_type" value="by_pair"/>
            <param name="inputs">
                <collection type="list:paired">
                    <element name="2">

                <element name="2" file="2.fastq"/>
                <element name="3" file="3.fastq"/>
                <element name="4" file="4.fastq"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- Test 7 paired collection concatenation by_strand with no other option -->
            <param name="input_type" value="paired_collection" />
            <param name="paired_cat_type" value="by_strand"/>
            <param name="inputs">
                <collection type="list:paired">
                    <element name="2">

            <output_collection name="paired_output" type="paired" >
                <element name="forward" file="f.fastq"/>
                <element name="reverse" file="r.fastq"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- Test 8 - 2 collections concatenation -->
            <param name="input_type" value="simple_collections" />
            <param name="input_1">
                <collection type="list">
                    <element name="2" value="2_f.fastq"/>
                    <element name="3" value="3_f.fastq"/>
                    <element name="4" value="4_f.fastq"/>

                <element name="2" file="2.fastq"/>
                <element name="3" file="3.fastq"/>
                <element name="4" file="4.fastq"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- Test 9 - 2 collections concatenation with other options-->
            <param name="input_type" value="simple_collections" />
            <param name="input_1">
                <collection type="list">
                    <element name="1_f.fastq.gz" value="1_f.fastq.gz"/>
                </collection>
            </param>

            <param name="headers" value="4" />
            <output_collection name="list_output" type="list" count="1" >
                <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- Test 10 nested collections concatenation -->
            <param name="input_type" value="nested_collection" />
            <param name="inputs">
                <collection type="list:list">
                    <element name="2">
                        <collection type="list">

            <output_collection name="list_output" type="list" count="2" >
                <element name="2" file="2.fastq"/>
                <element name="3" file="3.fastq"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- Test 11 nested collections concatenation with options and gzip-->
            <param name="input_type" value="nested_collection" />
            <param name="inputs">
                <collection type="list:list">
                    <element name="1">
                        <collection type="list">

-----

Adapted from galaxy's catWrapper.xml to allow multiple input files.

    </help>
    <citations>
        <citation type="doi">10.1186/gb-2010-11-8-r86</citation>
    </citations>
</tool>