Mercurial > repos > iuc > trycycler_cluster

comparison trycycler_cluster.xml @ 1:189e837009c9 draft

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"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
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0:c767a45616d0 1:189e837009c9
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>