Mercurial > repos > iuc > trycycler_cluster
comparison trycycler_cluster.xml @ 1:189e837009c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
author | iuc |
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date | Sat, 13 Feb 2021 17:32:01 +0000 |
parents | c767a45616d0 |
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0:c767a45616d0 | 1:189e837009c9 |
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1 <tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='21.01'> | 1 <tool id='trycycler_cluster' name='Trycycler cluster' version='@TOOL_VERSION@' profile='20.01'> |
2 <description>cluster the contigs of your input assemblies into per-replicon groups</description> | 2 <description>cluster the contigs of your input assemblies into per-replicon groups</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro='edam_ontology'/> | 6 <expand macro='edam_ontology' /> |
7 <expand macro='requirements'/> | 7 <expand macro='requirements' /> |
8 <version_command>trycycler --version</version_command> | 8 <version_command>trycycler --version</version_command> |
9 <command detect_errors='exit_code'><![CDATA[ | 9 <command detect_errors='exit_code'><![CDATA[ |
10 #import re | 10 #import re |
11 mkdir -p initial_clusters assemblies && | 11 mkdir -p initial_clusters assemblies && |
12 #for $input_file in $assemblies | 12 #for $input_file in $assemblies |
21 --threads \${GALAXY_SLOTS:-2} | 21 --threads \${GALAXY_SLOTS:-2} |
22 --out_dir 'initial_clusters' && | 22 --out_dir 'initial_clusters' && |
23 mv initial_clusters/contigs.phylip '$output_phylip' && | 23 mv initial_clusters/contigs.phylip '$output_phylip' && |
24 mv initial_clusters/contigs.newick '$output_newick' && | 24 mv initial_clusters/contigs.newick '$output_newick' && |
25 python3 '$__tool_directory__/trycycler.py' 'cluster' 'initial_clusters' | 25 python3 '$__tool_directory__/trycycler.py' 'cluster' 'initial_clusters' |
26 ]]></command> | 26 ]]> </command> |
27 <inputs> | 27 <inputs> |
28 <param name='assemblies' type='data' | 28 <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)' /> |
29 format='fasta,fasta.gz' multiple='true' label='Assembled sequences datasets' | 29 <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' /> |
30 help='Input assemblies whose contigs will be clustered (multiple FASTA files)' /> | 30 <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.' /> |
31 <param name='reads' type='data' | 31 <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.' /> |
32 format='fastq,fastq.gz' label='Long-read datasets' | 32 <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.' /> |
33 help='Long reads (FASTQ format) used to generate the assemblies' /> | |
34 <param argument='--min_contig_len' type='integer' | |
35 min='100' max='5000' value='1000' label='Minimun contig length' | |
36 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.' /> | |
37 <param argument='--min_contig_depth' type='float' | |
38 min='0.01' max='1' value='0.1' label='Minimun contig depth' | |
39 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.'/> | |
40 <param argument='--distance' type='float' | |
41 min='0.001' max='0.1' value='0.01' label='Mash distance threshold' | |
42 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.' /> | |
43 </inputs> | 33 </inputs> |
44 <outputs> | 34 <outputs> |
45 <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip'/> | 35 <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' /> |
46 <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick'/> | 36 <data name='output_newick' format='newick' label='${tool.name} on ${on_string}: newick' /> |
47 <collection name='initial_clusters' type='list' label='${tool.name} on ${on_string}'> | 37 <collection name='initial_clusters' type='list' label='${tool.name} on ${on_string}'> |
48 <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters'/> | 38 <discover_datasets pattern='__designation_and_ext__' format='fasta' directory='initial_clusters' /> |
49 </collection> | 39 </collection> |
50 </outputs> | 40 </outputs> |
51 <tests> | 41 <tests> |
52 <test> | 42 <test> |
53 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> | 43 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> |
54 <param name='reads' value='reads.fastq.gz'/> | 44 <param name='reads' value='reads.fastq.gz' /> |
55 <output name='output_phylip' file='contigs_01.phylip'/> | 45 <output name='output_phylip' file='contigs_01.phylip' /> |
56 <output name='output_newick' file='contigs_01.newick'/> | 46 <output name='output_newick' file='contigs_01.newick' /> |
57 <output_collection name='initial_clusters' type='list' count='2'> | 47 <output_collection name='initial_clusters' type='list' count='2'> |
58 <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20'/> | 48 <element name='cluster_01' file='cluster_01.fasta' ftype='fasta' lines_diff='20' /> |
59 </output_collection> | 49 </output_collection> |
60 </test> | 50 </test> |
61 <test> | 51 <test> |
62 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> | 52 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> |
63 <param name='reads' value='reads.fastq.gz'/> | 53 <param name='reads' value='reads.fastq.gz' /> |
64 <param name='min_contig_len' value='900'/> | 54 <param name='min_contig_len' value='900' /> |
65 <param name='min_contig_depth' value='0.05'/> | 55 <param name='min_contig_depth' value='0.05' /> |
66 <param name='distance' value='0.05'/> | 56 <param name='distance' value='0.05' /> |
67 <output name='output_phylip' file='contigs_02.phylip'/> | 57 <output name='output_phylip' file='contigs_02.phylip' /> |
68 <output name='output_newick' file='contigs_02.newick'/> | 58 <output name='output_newick' file='contigs_02.newick' /> |
69 <output_collection name='initial_clusters' type='list' count='2'> | 59 <output_collection name='initial_clusters' type='list' count='2'> |
70 <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20'/> | 60 <element name='cluster_01' file='cluster_02.fasta' ftype='fasta' lines_diff='20' /> |
71 </output_collection> | 61 </output_collection> |
72 </test> | 62 </test> |
73 <test> | 63 <test> |
74 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> | 64 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> |
75 <param name='reads' value='reads.fastq.gz'/> | 65 <param name='reads' value='reads.fastq.gz' /> |
76 <param name='min_contig_len' value='850'/> | 66 <param name='min_contig_len' value='850' /> |
77 <param name='min_contig_depth' value='0.01'/> | 67 <param name='min_contig_depth' value='0.01' /> |
78 <param name='distance' value='0.09'/> | 68 <param name='distance' value='0.09' /> |
79 <output name='output_phylip' file='contigs_03.phylip'/> | 69 <output name='output_phylip' file='contigs_03.phylip' /> |
80 <output name='output_newick' file='contigs_03.newick'/> | 70 <output name='output_newick' file='contigs_03.newick' /> |
81 <output_collection name='initial_clusters' type='list' count='2'> | 71 <output_collection name='initial_clusters' type='list' count='2'> |
82 <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20'/> | 72 <element name='cluster_01' file='cluster_03.fasta' ftype='fasta' lines_diff='20' /> |
83 </output_collection> | 73 </output_collection> |
84 </test> | 74 </test> |
85 <test> | 75 <test> |
86 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz'/> | 76 <param name='assemblies' value='assembly_00.fasta.gz,assembly_01.fasta.gz,assembly_02.fasta.gz,assembly_03.fasta.gz' /> |
87 <param name='reads' value='reads.fastq.gz'/> | 77 <param name='reads' value='reads.fastq.gz' /> |
88 <param name='min_contig_len' value='1100'/> | 78 <param name='min_contig_len' value='1100' /> |
89 <param name='min_contig_depth' value='0.02'/> | 79 <param name='min_contig_depth' value='0.02' /> |
90 <param name='distance' value='0.07'/> | 80 <param name='distance' value='0.07' /> |
91 <output name='output_phylip' file='contigs_04.phylip'/> | 81 <output name='output_phylip' file='contigs_04.phylip' /> |
92 <output name='output_newick' file='contigs_04.newick'/> | 82 <output name='output_newick' file='contigs_04.newick' /> |
93 <output_collection name='initial_clusters' type='list' count='2'> | 83 <output_collection name='initial_clusters' type='list' count='2'> |
94 <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20'/> | 84 <element name='cluster_01' file='cluster_04.fasta' ftype='fasta' lines_diff='20' /> |
95 </output_collection> | 85 </output_collection> |
96 </test> | 86 </test> |
97 </tests> | 87 </tests> |
98 <help><![CDATA[ | 88 <help><![CDATA[ |
99 .. class:: infomark | 89 .. class:: infomark |
100 | 90 |
101 **Purpose** | 91 **Purpose** |
142 ---- | 132 ---- |
143 | 133 |
144 .. class:: infomark | 134 .. class:: infomark |
145 | 135 |
146 @PIPELINE@ | 136 @PIPELINE@ |
147 ]]></help> | 137 ]]> </help> |
148 <expand macro='citations'/> | 138 <expand macro='citations' /> |
149 </tool> | 139 </tool> |