| Previous changeset 0:85658cabbbed (2021-02-11) Next changeset 2:cb4768eeca3b (2021-10-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912" |
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modified:
trycycler_subsample.xml |
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| diff -r 85658cabbbed -r 383bb5ad32e2 trycycler_subsample.xml --- a/trycycler_subsample.xml Thu Feb 11 19:25:20 2021 +0000 +++ b/trycycler_subsample.xml Sat Feb 13 17:30:32 2021 +0000 |
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| b"@@ -1,10 +1,10 @@\n-<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='21.01'>\n+<tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='20.01'>\n <description>make a maximally-independent read subsets of an appropiate depth for your genome</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro='edam_ontology'/>\n- <expand macro='requirements'/>\n+ <expand macro='edam_ontology' />\n+ <expand macro='requirements' />\n <version_command>trycycler --version</version_command>\n <command detect_errors='exit_code'><![CDATA[\n mkdir -p output_subsamples &&\n@@ -17,34 +17,21 @@\n --min_read_depth $min_read_depth\n --threads \\${GALAXY_SLOTS:-2}\n --out_dir output_subsamples\n- ]]></command>\n+ ]]> </command>\n <inputs>\n- <param name='reads' type='data' \n- format='fastq,fastq.gz' \n- label='Long-read dataset' help='--reads' />\n- <param argument='--count' type='integer' \n- min='2' max='20' \n- value='12' label='Number of subsampled reads set to output' \n- help='The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.' />\n+ <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read dataset' help='--reads' />\n+ <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.' />\n <conditional name='option'>\n- <param name='genome' type='select' \n- label='Provide an estimated genomoe size'\n- 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.' >\n- <option value='true'>Provide estimeted genome size</option>\n- <option value='false'>Run miniasm for estimating genome size</option>\n+ <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.' >\n+ <option value='true'>Provide estimeted genome size</option>\n+ <option value='false'>Run miniasm for estimating genome size</option>\n </param>\n- <when value='false'/>\n+ <when value='false' />\n <when value='true'>\n- <param argument='--genome_size' type='integer' \n- min='10000' max='15000000' \n- value='30000' label='Estimated total genome size' \n- help='An estimate of the isolate total genome size.' />\n+ <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.' />\n </when>\n </conditional>\n- <param argument='--min_read_depth' type='integer' min='15' max='120' \n- value='25' \n- label='Minimum subset read depth' \n- 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.' />\n+ <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.' />\n </"..b"amples_fastq' type='list' count='5'>\n- <element name='sample_01' file='sample_01_03.fastq' ftype='fastq'/>\n- <element name='sample_02' file='sample_02_03.fastq' ftype='fastq'/>\n- <element name='sample_03' file='sample_03_03.fastq' ftype='fastq'/>\n- <element name='sample_04' file='sample_04_03.fastq' ftype='fastq'/>\n- <element name='sample_05' file='sample_05_03.fastq' ftype='fastq'/>\n+ <element name='sample_01' file='sample_01_03.fastq' ftype='fastq' />\n+ <element name='sample_02' file='sample_02_03.fastq' ftype='fastq' />\n+ <element name='sample_03' file='sample_03_03.fastq' ftype='fastq' />\n+ <element name='sample_04' file='sample_04_03.fastq' ftype='fastq' />\n+ <element name='sample_05' file='sample_05_03.fastq' ftype='fastq' />\n </output_collection>\n </test>\n <test>\n- <param name='reads' value='reads.fastq.gz'/>\n+ <param name='reads' value='reads.fastq.gz' />\n <conditional name='option'>\n- <param name='genome' value='true'/>\n- <param name='genome_size' value='10000'/>\n+ <param name='genome' value='true' />\n+ <param name='genome_size' value='10000' />\n </conditional>\n- <param name='min_read_depth' value='30'/>\n- <param name='count' value='12'/>\n+ <param name='min_read_depth' value='30' />\n+ <param name='count' value='12' />\n <output_collection name='subsamples_fastq' type='list' count='12'>\n- <element name='sample_01' file='sample_01_04.fastq' ftype='fastq'/>\n- <element name='sample_02' file='sample_02_04.fastq' ftype='fastq'/>\n- <element name='sample_03' file='sample_03_04.fastq' ftype='fastq'/>\n- <element name='sample_04' file='sample_04_04.fastq' ftype='fastq'/>\n- <element name='sample_05' file='sample_05_04.fastq' ftype='fastq'/>\n- <element name='sample_06' file='sample_06_04.fastq' ftype='fastq'/>\n- <element name='sample_07' file='sample_07_04.fastq' ftype='fastq'/>\n- <element name='sample_08' file='sample_08_04.fastq' ftype='fastq'/>\n- <element name='sample_09' file='sample_09_04.fastq' ftype='fastq'/>\n- <element name='sample_10' file='sample_10_04.fastq' ftype='fastq'/>\n- <element name='sample_11' file='sample_11_04.fastq' ftype='fastq'/>\n- <element name='sample_12' file='sample_12_04.fastq' ftype='fastq'/>\n+ <element name='sample_01' file='sample_01_04.fastq' ftype='fastq' />\n+ <element name='sample_02' file='sample_02_04.fastq' ftype='fastq' />\n+ <element name='sample_03' file='sample_03_04.fastq' ftype='fastq' />\n+ <element name='sample_04' file='sample_04_04.fastq' ftype='fastq' />\n+ <element name='sample_05' file='sample_05_04.fastq' ftype='fastq' />\n+ <element name='sample_06' file='sample_06_04.fastq' ftype='fastq' />\n+ <element name='sample_07' file='sample_07_04.fastq' ftype='fastq' />\n+ <element name='sample_08' file='sample_08_04.fastq' ftype='fastq' />\n+ <element name='sample_09' file='sample_09_04.fastq' ftype='fastq' />\n+ <element name='sample_10' file='sample_10_04.fastq' ftype='fastq' />\n+ <element name='sample_11' file='sample_11_04.fastq' ftype='fastq' />\n+ <element name='sample_12' file='sample_12_04.fastq' ftype='fastq' />\n </output_collection>\n- </test> \n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n@@ -153,6 +140,6 @@\n .. class:: infomark\n \n @PIPELINE@\n- ]]></help>\n- <expand macro='citations'/>\n+ ]]> </help>\n+ <expand macro='citations' />\n </tool>\n" |