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Changeset 1:189e837009c9 (2021-02-13)

Previous changeset 0:c767a45616d0 (2021-02-11) Next changeset 2:6f4c8ad6ea01 (2021-10-04)

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

modified:
trycycler_cluster.xml

diff -r c767a45616d0 -r 189e837009c9 trycycler_cluster.xml
--- a/trycycler_cluster.xml Thu Feb 11 19:26:49 2021 +0000
+++ b/trycycler_cluster.xml Sat Feb 13 17:32:01 2021 +0000

[

b"@@ -1,10 +1,10 @@\n-<tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='21.01'>\n+<tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='20.01'>\n <description>cluster the contigs of your input assemblies into per-replicon groups</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 #import re\n@@ -23,77 +23,67 @@\n mv initial_clusters/contigs.phylip '$output_phylip' &&\n mv initial_clusters/contigs.newick '$output_newick' && \n python3 '$__tool_directory__/trycycler.py' 'cluster' 'initial_clusters'\n- ]]></command>\n+ ]]> </command>\n <inputs>\n- <param name='assemblies' type='data' \n- format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets' \n- help='Input assemblies whose contigs will be clustered (multiple FASTA files)' />\n- <param name='reads' type='data' \n- format='fastq,fastq.gz' label='Long-read datasets' \n- help='Long reads (FASTQ format) used to generate the assemblies' />\n- <param argument='--min_contig_len' type='integer' \n- min='100' max='5000' value='1000' label='Minimun contig length' \n- 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.' />\n- <param argument='--min_contig_depth' type='float' \n- min='0.01' max='1' value='0.1' label='Minimun contig depth' \n- 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.'/> \n- <param argument='--distance' type='float' \n- min='0.001' max='0.1' value='0.01' label='Mash distance threshold' \n- 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.' />\n+ <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)' />\n+ <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' />\n+ <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.' />\n+ <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.' />\n+ <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 "..b"aram name='min_contig_depth' value='0.05'/>\n- <param name='distance' value='0.05'/>\n- <output name='output_phylip' file='contigs_02.phylip'/>\n- <output name='output_newick' file='contigs_02.newick'/>\n+ <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_contig_len' value='900' />\n+ <param name='min_contig_depth' value='0.05' />\n+ <param name='distance' value='0.05' />\n+ <output name='output_phylip' file='contigs_02.phylip' />\n+ <output name='output_newick' file='contigs_02.newick' />\n <output_collection name='initial_clusters' type='list' count='2'>\n- <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20'/>\n+ <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20' />\n </output_collection>\n </test>\n <test>\n- <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>\n- <param name='reads' value='reads.fastq.gz'/>\n- <param name='min_contig_len' value='850'/>\n- <param name='min_contig_depth' value='0.01'/>\n- <param name='distance' value='0.09'/>\n- <output name='output_phylip' file='contigs_03.phylip'/>\n- <output name='output_newick' file='contigs_03.newick'/>\n+ <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_contig_len' value='850' />\n+ <param name='min_contig_depth' value='0.01' />\n+ <param name='distance' value='0.09' />\n+ <output name='output_phylip' file='contigs_03.phylip' />\n+ <output name='output_newick' file='contigs_03.newick' />\n <output_collection name='initial_clusters' type='list' count='2'>\n- <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20'/>\n+ <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20' />\n </output_collection>\n </test>\n <test>\n- <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/>\n- <param name='reads' value='reads.fastq.gz'/>\n- <param name='min_contig_len' value='1100'/>\n- <param name='min_contig_depth' value='0.02'/>\n- <param name='distance' value='0.07'/>\n- <output name='output_phylip' file='contigs_04.phylip'/>\n- <output name='output_newick' file='contigs_04.newick'/>\n+ <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_contig_len' value='1100' />\n+ <param name='min_contig_depth' value='0.02' />\n+ <param name='distance' value='0.07' />\n+ <output name='output_phylip' file='contigs_04.phylip' />\n+ <output name='output_newick' file='contigs_04.newick' />\n <output_collection name='initial_clusters' type='list' count='2'>\n- <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20'/>\n+ <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20' />\n </output_collection>\n- </test> \n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n@@ -144,6 +134,6 @@\n .. class:: infomark\n \n @PIPELINE@\n- ]]></help>\n- <expand macro='citations'/>\n+ ]]> </help>\n+ <expand macro='citations' />\n </tool>\n"