Mercurial > repos > iuc > trycycler_cluster
changeset 1:189e837009c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
| author | iuc |
|---|---|
| date | Sat, 13 Feb 2021 17:32:01 +0000 |
| parents | c767a45616d0 |
| children | 6f4c8ad6ea01 |
| files | trycycler_cluster.xml |
| diffstat | 1 files changed, 44 insertions(+), 54 deletions(-) [+] |
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--- a/trycycler_cluster.xml Thu Feb 11 19:26:49 2021 +0000 +++ b/trycycler_cluster.xml Sat Feb 13 17:32:01 2021 +0000 @@ -1,10 +1,10 @@ -<tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='21.01'> +<tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='20.01'> <description>cluster the contigs of your input assemblies into per-replicon groups</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[ #import re @@ -23,77 +23,67 @@ mv initial_clusters/contigs.phylip '$output_phylip' && mv initial_clusters/contigs.newick '$output_newick' && python3 '$__tool_directory__/trycycler.py' 'cluster' 'initial_clusters' - ]]></command> + ]]> </command> <inputs> - <param name='assemblies' type='data' - format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets' - help='Input assemblies whose contigs will be clustered (multiple FASTA files)' /> - <param name='reads' type='data' - format='fastq,fastq.gz' label='Long-read datasets' - help='Long reads (FASTQ format) used to generate the assemblies' /> - <param argument='--min_contig_len' type='integer' - min='100' max='5000' value='1000' label='Minimun contig length' - help='Contigs shorter than this are thrown out on the assumption that they are either incomplete or spurious. The default value is 1000, as plasmids smaller than that are very rare.' /> - <param argument='--min_contig_depth' type='float' - min='0.01' max='1' value='0.1' label='Minimun contig depth' - help='This controls how Trycycler filters out contigs with a low read depth. It is a multiple of the mean read depth for the assembly. For example, if an assembly has a mean depth of 90x and this setting is 0.1 (the default), then any contig with depth lower that x9 will be removed.'/> - <param argument='--distance' type='float' - min='0.001' max='0.1' value='0.01' label='Mash distance threshold' - help='This is the Mash distance threshold used when defining clusters, and the default threshold is 0.01. Smaller thresholds (e.g. 0.005) can result in a larger number of tighter clusters. Larger thresholds (e.g. 0.02) can result in a smaller number of looser clusters.' /> + <param name='assemblies' type='data' format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets' help='Input assemblies whose contigs will be clustered (multiple FASTA files)' /> + <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' /> + <param argument='--min_contig_len' type='integer' min='100' max='5000' value='1000' label='Minimun contig length' help='Contigs shorter than this are thrown out on the assumption that they are either incomplete or spurious. The default value is 1000, as plasmids smaller than that are very rare.' /> + <param argument='--min_contig_depth' type='float' min='0.01' max='1' value='0.1' label='Minimun contig depth' help='This controls how Trycycler filters out contigs with a low read depth. It is a multiple of the mean read depth for the assembly. For example, if an assembly has a mean depth of 90x and this setting is 0.1 (the default), then any contig with depth lower that x9 will be removed.' /> + <param argument='--distance' type='float' min='0.001' max='0.1' value='0.01' label='Mash distance threshold' help='This is the Mash distance threshold used when defining clusters, and the default threshold is 0.01. Smaller thresholds (e.g. 0.005) can result in a larger number of tighter clusters. Larger thresholds (e.g. 0.02) can result in a smaller number of looser clusters.' /> </inputs> <outputs> - <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip'/> - <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick'/> + <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' /> + <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick' /> <collection name='initial_clusters' type='list' label='${tool.name} on ${on_string}'> - <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters'/> + <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters' /> </collection> </outputs> <tests> <test> - <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> - <param name='reads' value='reads.fastq.gz'/> - <output name='output_phylip' file='contigs_01.phylip'/> - <output name='output_newick' file='contigs_01.newick'/> + <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> + <param name='reads' value='reads.fastq.gz' /> + <output name='output_phylip' file='contigs_01.phylip' /> + <output name='output_newick' file='contigs_01.newick' /> <output_collection name='initial_clusters' type='list' count='2'> - <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20'/> + <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20' /> </output_collection> </test> <test> - <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_contig_len' value='900'/> - <param name='min_contig_depth' value='0.05'/> - <param name='distance' value='0.05'/> - <output name='output_phylip' file='contigs_02.phylip'/> - <output name='output_newick' file='contigs_02.newick'/> + <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_contig_len' value='900' /> + <param name='min_contig_depth' value='0.05' /> + <param name='distance' value='0.05' /> + <output name='output_phylip' file='contigs_02.phylip' /> + <output name='output_newick' file='contigs_02.newick' /> <output_collection name='initial_clusters' type='list' count='2'> - <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20'/> + <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20' /> </output_collection> </test> <test> - <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_contig_len' value='850'/> - <param name='min_contig_depth' value='0.01'/> - <param name='distance' value='0.09'/> - <output name='output_phylip' file='contigs_03.phylip'/> - <output name='output_newick' file='contigs_03.newick'/> + <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_contig_len' value='850' /> + <param name='min_contig_depth' value='0.01' /> + <param name='distance' value='0.09' /> + <output name='output_phylip' file='contigs_03.phylip' /> + <output name='output_newick' file='contigs_03.newick' /> <output_collection name='initial_clusters' type='list' count='2'> - <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20'/> + <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20' /> </output_collection> </test> <test> - <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_contig_len' value='1100'/> - <param name='min_contig_depth' value='0.02'/> - <param name='distance' value='0.07'/> - <output name='output_phylip' file='contigs_04.phylip'/> - <output name='output_newick' file='contigs_04.newick'/> + <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_contig_len' value='1100' /> + <param name='min_contig_depth' value='0.02' /> + <param name='distance' value='0.07' /> + <output name='output_phylip' file='contigs_04.phylip' /> + <output name='output_newick' file='contigs_04.newick' /> <output_collection name='initial_clusters' type='list' count='2'> - <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20'/> + <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20' /> </output_collection> - </test> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -144,6 +134,6 @@ .. class:: infomark @PIPELINE@ - ]]></help> - <expand macro='citations'/> + ]]> </help> + <expand macro='citations' /> </tool>