comparison trycycler_subsample.xml @ 1:383bb5ad32e2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"

0:85658cabbbed

<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='21.01'>
    <description>make a maximally-independent read subsets of an appropiate depth for your genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='edam_ontology'/>
    <expand macro='requirements'/>
    <version_command>trycycler --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
        mkdir -p output_subsamples &&
        trycycler subsample
            --reads '${reads}'

                --genome_size $option.genome_size
            #end if
            --min_read_depth $min_read_depth
            --threads \${GALAXY_SLOTS:-2}
            --out_dir output_subsamples
    ]]></command>
    <inputs>
        <param name='reads' type='data' 
            format='fastq,fastq.gz'  
            label='Long-read dataset' help='--reads' />
        <param argument='--count' type='integer' 
            min='2' max='20' 
            value='12' label='Number of subsampled reads set to output' 
            help='The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.' />
        <conditional name='option'>
            <param name='genome' type='select' 
                label='Provide an estimated genomoe size'
                help='If you do not provide this, Trycycler subsample will run miniasm to quickly assemble your read set to get a size. This value is used to calculate read depths and does not need to be exact, e.g. 10% error is fine.' >
                    <option value='true'>Provide estimeted genome size</option>
                    <option value='false'>Run miniasm for estimating genome size</option>
            </param>
            <when value='false'/>
            <when value='true'>
                <param argument='--genome_size' type='integer' 
                    min='10000' max='15000000' 
                    value='30000' label='Estimated total genome size' 
                    help='An estimate of the isolate total genome size.' />
            </when>
        </conditional>
        <param argument='--min_read_depth' type='integer' min='15' max='120' 
            value='25' 
            label='Minimum subset read depth' 
            help='This is the minimum allowed read depth and also controls the subsampled depths. If is not provided, Trycycle decides what read depth each subset will be.' />
    </inputs>
    <outputs>
        <collection name='subsamples_fastq' type='list'>
            <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='output_subsamples'  />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name='reads' value='reads.fastq.gz'/>
            <conditional name='option'>
                <param name='genome' value='true'/>
                <param name='genome_size' value='10000'/>
            </conditional>
            <param name='min_read_depth' value='20'/>
            <param name='count' value='4'/>
            <output_collection name='subsamples_fastq' type='list' count='4'>
                <element name='sample_01' file='sample_01_01.fastq' ftype='fastq'/>
                <element name='sample_02' file='sample_02_01.fastq' ftype='fastq'/>
                <element name='sample_03' file='sample_03_01.fastq' ftype='fastq'/>
                <element name='sample_04' file='sample_04_01.fastq' ftype='fastq'/>
            </output_collection>
        </test>
        <test>
            <param name='reads' value='reads.fastq.gz'/>
            <conditional name='option'>
                <param name='genome' value='true'/>
                <param name='genome_size' value='10000'/>
            </conditional>
            <param name='min_read_depth' value='22'/>
            <param name='count' value='6'/>
            <output_collection name='subsamples_fastq' type='list' count='6'>
                <element name='sample_01' file='sample_01_02.fastq' ftype='fastq'/>
                <element name='sample_02' file='sample_02_02.fastq' ftype='fastq'/>
                <element name='sample_03' file='sample_03_02.fastq' ftype='fastq'/>
                <element name='sample_04' file='sample_04_02.fastq' ftype='fastq'/>
                <element name='sample_05' file='sample_05_02.fastq' ftype='fastq'/>
                <element name='sample_06' file='sample_06_02.fastq' ftype='fastq'/>
            </output_collection>
        </test>
        <test>
            <param name='reads' value='reads.fastq.gz'/>
            <conditional name='option'>
                <param name='genome' value='true'/>
                <param name='genome_size' value='10000'/>
            </conditional>
            <param name='min_read_depth' value='25'/>
            <param name='count' value='5'/>
            <output_collection name='subsamples_fastq' type='list' count='5'>
                <element name='sample_01' file='sample_01_03.fastq' ftype='fastq'/>
                <element name='sample_02' file='sample_02_03.fastq' ftype='fastq'/>
                <element name='sample_03' file='sample_03_03.fastq' ftype='fastq'/>
                <element name='sample_04' file='sample_04_03.fastq' ftype='fastq'/>
                <element name='sample_05' file='sample_05_03.fastq' ftype='fastq'/>
            </output_collection>
        </test>
        <test>
            <param name='reads' value='reads.fastq.gz'/>
            <conditional name='option'>
                <param name='genome' value='true'/>
                <param name='genome_size' value='10000'/>
            </conditional>
            <param name='min_read_depth' value='30'/>
            <param name='count' value='12'/>
            <output_collection name='subsamples_fastq' type='list' count='12'>
                <element name='sample_01' file='sample_01_04.fastq' ftype='fastq'/>
                <element name='sample_02' file='sample_02_04.fastq' ftype='fastq'/>
                <element name='sample_03' file='sample_03_04.fastq' ftype='fastq'/>
                <element name='sample_04' file='sample_04_04.fastq' ftype='fastq'/>
                <element name='sample_05' file='sample_05_04.fastq' ftype='fastq'/>
                <element name='sample_06' file='sample_06_04.fastq' ftype='fastq'/>
                <element name='sample_07' file='sample_07_04.fastq' ftype='fastq'/>
                <element name='sample_08' file='sample_08_04.fastq' ftype='fastq'/>
                <element name='sample_09' file='sample_09_04.fastq' ftype='fastq'/>
                <element name='sample_10' file='sample_10_04.fastq' ftype='fastq'/>
                <element name='sample_11' file='sample_11_04.fastq' ftype='fastq'/>
                <element name='sample_12' file='sample_12_04.fastq' ftype='fastq'/>
            </output_collection>
        </test> 
    </tests>
    <help><![CDATA[
.. class:: infomark

**Purpose**

----                                                                                                    
                                                                                                        
.. class:: infomark

@PIPELINE@
    ]]></help>
    <expand macro='citations'/>
</tool>

1:383bb5ad32e2

<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='20.01'>
    <description>make a maximally-independent read subsets of an appropiate depth for your genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <version_command>trycycler --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
        mkdir -p output_subsamples &&
        trycycler subsample
            --reads '${reads}'

                --genome_size $option.genome_size
            #end if
            --min_read_depth $min_read_depth
            --threads \${GALAXY_SLOTS:-2}
            --out_dir output_subsamples
    ]]>    </command>
    <inputs>
        <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read dataset' help='--reads' />
        <param argument='--count' type='integer' min='2' max='20' value='12' label='Number of subsampled reads set to output' help='The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.' />
        <conditional name='option'>
            <param name='genome' type='select' label='Provide an estimated genomoe size' help='If you do not provide this, Trycycler subsample will run miniasm to quickly assemble your read set to get a size. This value is used to calculate read depths and does not need to be exact, e.g. 10% error is fine.' >
                <option value='true'>Provide estimeted genome size</option>
                <option value='false'>Run miniasm for estimating genome size</option>
            </param>
            <when value='false' />
            <when value='true'>
                <param argument='--genome_size' type='integer' min='10000' max='15000000' value='30000' label='Estimated total genome size' help='An estimate of the isolate total genome size.' />
            </when>
        </conditional>
        <param argument='--min_read_depth' type='integer' min='15' max='120' value='25' label='Minimum subset read depth' help='This is the minimum allowed read depth and also controls the subsampled depths. If is not provided, Trycycle decides what read depth each subset will be.' />
    </inputs>
    <outputs>
        <collection name='subsamples_fastq' type='list'>
            <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='output_subsamples'  />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name='reads' value='reads.fastq.gz' />
            <conditional name='option'>
                <param name='genome' value='true' />
                <param name='genome_size' value='10000' />
            </conditional>
            <param name='min_read_depth' value='20' />
            <param name='count' value='4' />
            <output_collection name='subsamples_fastq' type='list' count='4'>
                <element name='sample_01' file='sample_01_01.fastq' ftype='fastq' />
                <element name='sample_02' file='sample_02_01.fastq' ftype='fastq' />
                <element name='sample_03' file='sample_03_01.fastq' ftype='fastq' />
                <element name='sample_04' file='sample_04_01.fastq' ftype='fastq' />
            </output_collection>
        </test>
        <test>
            <param name='reads' value='reads.fastq.gz' />
            <conditional name='option'>
                <param name='genome' value='true' />
                <param name='genome_size' value='10000' />
            </conditional>
            <param name='min_read_depth' value='22' />
            <param name='count' value='6' />
            <output_collection name='subsamples_fastq' type='list' count='6'>
                <element name='sample_01' file='sample_01_02.fastq' ftype='fastq' />
                <element name='sample_02' file='sample_02_02.fastq' ftype='fastq' />
                <element name='sample_03' file='sample_03_02.fastq' ftype='fastq' />
                <element name='sample_04' file='sample_04_02.fastq' ftype='fastq' />
                <element name='sample_05' file='sample_05_02.fastq' ftype='fastq' />
                <element name='sample_06' file='sample_06_02.fastq' ftype='fastq' />
            </output_collection>
        </test>
        <test>
            <param name='reads' value='reads.fastq.gz' />
            <conditional name='option'>
                <param name='genome' value='true' />
                <param name='genome_size' value='10000' />
            </conditional>
            <param name='min_read_depth' value='25' />
            <param name='count' value='5' />
            <output_collection name='subsamples_fastq' type='list' count='5'>
                <element name='sample_01' file='sample_01_03.fastq' ftype='fastq' />
                <element name='sample_02' file='sample_02_03.fastq' ftype='fastq' />
                <element name='sample_03' file='sample_03_03.fastq' ftype='fastq' />
                <element name='sample_04' file='sample_04_03.fastq' ftype='fastq' />
                <element name='sample_05' file='sample_05_03.fastq' ftype='fastq' />
            </output_collection>
        </test>
        <test>
            <param name='reads' value='reads.fastq.gz' />
            <conditional name='option'>
                <param name='genome' value='true' />
                <param name='genome_size' value='10000' />
            </conditional>
            <param name='min_read_depth' value='30' />
            <param name='count' value='12' />
            <output_collection name='subsamples_fastq' type='list' count='12'>
                <element name='sample_01' file='sample_01_04.fastq' ftype='fastq' />
                <element name='sample_02' file='sample_02_04.fastq' ftype='fastq' />
                <element name='sample_03' file='sample_03_04.fastq' ftype='fastq' />
                <element name='sample_04' file='sample_04_04.fastq' ftype='fastq' />
                <element name='sample_05' file='sample_05_04.fastq' ftype='fastq' />
                <element name='sample_06' file='sample_06_04.fastq' ftype='fastq' />
                <element name='sample_07' file='sample_07_04.fastq' ftype='fastq' />
                <element name='sample_08' file='sample_08_04.fastq' ftype='fastq' />
                <element name='sample_09' file='sample_09_04.fastq' ftype='fastq' />
                <element name='sample_10' file='sample_10_04.fastq' ftype='fastq' />
                <element name='sample_11' file='sample_11_04.fastq' ftype='fastq' />
                <element name='sample_12' file='sample_12_04.fastq' ftype='fastq' />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**Purpose**

----                                                                                                    
                                                                                                        
.. class:: infomark

@PIPELINE@
    ]]>    </help>
    <expand macro='citations' />
</tool>