Mercurial > repos > iuc > trycycler_subsample
changeset 1:383bb5ad32e2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
| author | iuc |
|---|---|
| date | Sat, 13 Feb 2021 17:30:32 +0000 |
| parents | 85658cabbbed |
| children | cb4768eeca3b |
| files | trycycler_subsample.xml |
| diffstat | 1 files changed, 62 insertions(+), 75 deletions(-) [+] |
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--- a/trycycler_subsample.xml Thu Feb 11 19:25:20 2021 +0000 +++ b/trycycler_subsample.xml Sat Feb 13 17:30:32 2021 +0000 @@ -1,10 +1,10 @@ -<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='21.01'> +<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'/> + <expand macro='edam_ontology' /> + <expand macro='requirements' /> <version_command>trycycler --version</version_command> <command detect_errors='exit_code'><![CDATA[ mkdir -p output_subsamples && @@ -17,34 +17,21 @@ --min_read_depth $min_read_depth --threads \${GALAXY_SLOTS:-2} --out_dir output_subsamples - ]]></command> + ]]> </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.' /> + <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 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='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.' /> + <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.' /> + <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'> @@ -53,76 +40,76 @@ </outputs> <tests> <test> - <param name='reads' value='reads.fastq.gz'/> + <param name='reads' value='reads.fastq.gz' /> <conditional name='option'> - <param name='genome' value='true'/> - <param name='genome_size' value='10000'/> + <param name='genome' value='true' /> + <param name='genome_size' value='10000' /> </conditional> - <param name='min_read_depth' value='20'/> - <param name='count' value='4'/> + <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'/> + <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'/> + <param name='reads' value='reads.fastq.gz' /> <conditional name='option'> - <param name='genome' value='true'/> - <param name='genome_size' value='10000'/> + <param name='genome' value='true' /> + <param name='genome_size' value='10000' /> </conditional> - <param name='min_read_depth' value='22'/> - <param name='count' value='6'/> + <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'/> + <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'/> + <param name='reads' value='reads.fastq.gz' /> <conditional name='option'> - <param name='genome' value='true'/> - <param name='genome_size' value='10000'/> + <param name='genome' value='true' /> + <param name='genome_size' value='10000' /> </conditional> - <param name='min_read_depth' value='25'/> - <param name='count' value='5'/> + <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'/> + <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'/> + <param name='reads' value='reads.fastq.gz' /> <conditional name='option'> - <param name='genome' value='true'/> - <param name='genome_size' value='10000'/> + <param name='genome' value='true' /> + <param name='genome_size' value='10000' /> </conditional> - <param name='min_read_depth' value='30'/> - <param name='count' value='12'/> + <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'/> + <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> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -153,6 +140,6 @@ .. class:: infomark @PIPELINE@ - ]]></help> - <expand macro='citations'/> + ]]> </help> + <expand macro='citations' /> </tool>