Mercurial > repos > iuc > trycycler_subsample
comparison trycycler_subsample.xml @ 1:383bb5ad32e2 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 17:30:32 +0000 |
parents | 85658cabbbed |
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0:85658cabbbed | 1:383bb5ad32e2 |
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1 <tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='21.01'> | 1 <tool id='trycycler_subsample' name='Trycycler subsample' version='@TOOL_VERSION@' profile='20.01'> |
2 <description>make a maximally-independent read subsets of an appropiate depth for your genome</description> | 2 <description>make a maximally-independent read subsets of an appropiate depth for your genome</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 mkdir -p output_subsamples && | 10 mkdir -p output_subsamples && |
11 trycycler subsample | 11 trycycler subsample |
12 --reads '${reads}' | 12 --reads '${reads}' |
15 --genome_size $option.genome_size | 15 --genome_size $option.genome_size |
16 #end if | 16 #end if |
17 --min_read_depth $min_read_depth | 17 --min_read_depth $min_read_depth |
18 --threads \${GALAXY_SLOTS:-2} | 18 --threads \${GALAXY_SLOTS:-2} |
19 --out_dir output_subsamples | 19 --out_dir output_subsamples |
20 ]]></command> | 20 ]]> </command> |
21 <inputs> | 21 <inputs> |
22 <param name='reads' type='data' | 22 <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read dataset' help='--reads' /> |
23 format='fastq,fastq.gz' | 23 <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.' /> |
24 label='Long-read dataset' help='--reads' /> | |
25 <param argument='--count' type='integer' | |
26 min='2' max='20' | |
27 value='12' label='Number of subsampled reads set to output' | |
28 help='The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.' /> | |
29 <conditional name='option'> | 24 <conditional name='option'> |
30 <param name='genome' type='select' | 25 <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.' > |
31 label='Provide an estimated genomoe size' | 26 <option value='true'>Provide estimeted genome size</option> |
32 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.' > | 27 <option value='false'>Run miniasm for estimating genome size</option> |
33 <option value='true'>Provide estimeted genome size</option> | |
34 <option value='false'>Run miniasm for estimating genome size</option> | |
35 </param> | 28 </param> |
36 <when value='false'/> | 29 <when value='false' /> |
37 <when value='true'> | 30 <when value='true'> |
38 <param argument='--genome_size' type='integer' | 31 <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.' /> |
39 min='10000' max='15000000' | |
40 value='30000' label='Estimated total genome size' | |
41 help='An estimate of the isolate total genome size.' /> | |
42 </when> | 32 </when> |
43 </conditional> | 33 </conditional> |
44 <param argument='--min_read_depth' type='integer' min='15' max='120' | 34 <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.' /> |
45 value='25' | |
46 label='Minimum subset read depth' | |
47 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.' /> | |
48 </inputs> | 35 </inputs> |
49 <outputs> | 36 <outputs> |
50 <collection name='subsamples_fastq' type='list'> | 37 <collection name='subsamples_fastq' type='list'> |
51 <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='output_subsamples' /> | 38 <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='output_subsamples' /> |
52 </collection> | 39 </collection> |
53 </outputs> | 40 </outputs> |
54 <tests> | 41 <tests> |
55 <test> | 42 <test> |
56 <param name='reads' value='reads.fastq.gz'/> | 43 <param name='reads' value='reads.fastq.gz' /> |
57 <conditional name='option'> | 44 <conditional name='option'> |
58 <param name='genome' value='true'/> | 45 <param name='genome' value='true' /> |
59 <param name='genome_size' value='10000'/> | 46 <param name='genome_size' value='10000' /> |
60 </conditional> | 47 </conditional> |
61 <param name='min_read_depth' value='20'/> | 48 <param name='min_read_depth' value='20' /> |
62 <param name='count' value='4'/> | 49 <param name='count' value='4' /> |
63 <output_collection name='subsamples_fastq' type='list' count='4'> | 50 <output_collection name='subsamples_fastq' type='list' count='4'> |
64 <element name='sample_01' file='sample_01_01.fastq' ftype='fastq'/> | 51 <element name='sample_01' file='sample_01_01.fastq' ftype='fastq' /> |
65 <element name='sample_02' file='sample_02_01.fastq' ftype='fastq'/> | 52 <element name='sample_02' file='sample_02_01.fastq' ftype='fastq' /> |
66 <element name='sample_03' file='sample_03_01.fastq' ftype='fastq'/> | 53 <element name='sample_03' file='sample_03_01.fastq' ftype='fastq' /> |
67 <element name='sample_04' file='sample_04_01.fastq' ftype='fastq'/> | 54 <element name='sample_04' file='sample_04_01.fastq' ftype='fastq' /> |
68 </output_collection> | 55 </output_collection> |
69 </test> | 56 </test> |
70 <test> | 57 <test> |
71 <param name='reads' value='reads.fastq.gz'/> | 58 <param name='reads' value='reads.fastq.gz' /> |
72 <conditional name='option'> | 59 <conditional name='option'> |
73 <param name='genome' value='true'/> | 60 <param name='genome' value='true' /> |
74 <param name='genome_size' value='10000'/> | 61 <param name='genome_size' value='10000' /> |
75 </conditional> | 62 </conditional> |
76 <param name='min_read_depth' value='22'/> | 63 <param name='min_read_depth' value='22' /> |
77 <param name='count' value='6'/> | 64 <param name='count' value='6' /> |
78 <output_collection name='subsamples_fastq' type='list' count='6'> | 65 <output_collection name='subsamples_fastq' type='list' count='6'> |
79 <element name='sample_01' file='sample_01_02.fastq' ftype='fastq'/> | 66 <element name='sample_01' file='sample_01_02.fastq' ftype='fastq' /> |
80 <element name='sample_02' file='sample_02_02.fastq' ftype='fastq'/> | 67 <element name='sample_02' file='sample_02_02.fastq' ftype='fastq' /> |
81 <element name='sample_03' file='sample_03_02.fastq' ftype='fastq'/> | 68 <element name='sample_03' file='sample_03_02.fastq' ftype='fastq' /> |
82 <element name='sample_04' file='sample_04_02.fastq' ftype='fastq'/> | 69 <element name='sample_04' file='sample_04_02.fastq' ftype='fastq' /> |
83 <element name='sample_05' file='sample_05_02.fastq' ftype='fastq'/> | 70 <element name='sample_05' file='sample_05_02.fastq' ftype='fastq' /> |
84 <element name='sample_06' file='sample_06_02.fastq' ftype='fastq'/> | 71 <element name='sample_06' file='sample_06_02.fastq' ftype='fastq' /> |
85 </output_collection> | 72 </output_collection> |
86 </test> | 73 </test> |
87 <test> | 74 <test> |
88 <param name='reads' value='reads.fastq.gz'/> | 75 <param name='reads' value='reads.fastq.gz' /> |
89 <conditional name='option'> | 76 <conditional name='option'> |
90 <param name='genome' value='true'/> | 77 <param name='genome' value='true' /> |
91 <param name='genome_size' value='10000'/> | 78 <param name='genome_size' value='10000' /> |
92 </conditional> | 79 </conditional> |
93 <param name='min_read_depth' value='25'/> | 80 <param name='min_read_depth' value='25' /> |
94 <param name='count' value='5'/> | 81 <param name='count' value='5' /> |
95 <output_collection name='subsamples_fastq' type='list' count='5'> | 82 <output_collection name='subsamples_fastq' type='list' count='5'> |
96 <element name='sample_01' file='sample_01_03.fastq' ftype='fastq'/> | 83 <element name='sample_01' file='sample_01_03.fastq' ftype='fastq' /> |
97 <element name='sample_02' file='sample_02_03.fastq' ftype='fastq'/> | 84 <element name='sample_02' file='sample_02_03.fastq' ftype='fastq' /> |
98 <element name='sample_03' file='sample_03_03.fastq' ftype='fastq'/> | 85 <element name='sample_03' file='sample_03_03.fastq' ftype='fastq' /> |
99 <element name='sample_04' file='sample_04_03.fastq' ftype='fastq'/> | 86 <element name='sample_04' file='sample_04_03.fastq' ftype='fastq' /> |
100 <element name='sample_05' file='sample_05_03.fastq' ftype='fastq'/> | 87 <element name='sample_05' file='sample_05_03.fastq' ftype='fastq' /> |
101 </output_collection> | 88 </output_collection> |
102 </test> | 89 </test> |
103 <test> | 90 <test> |
104 <param name='reads' value='reads.fastq.gz'/> | 91 <param name='reads' value='reads.fastq.gz' /> |
105 <conditional name='option'> | 92 <conditional name='option'> |
106 <param name='genome' value='true'/> | 93 <param name='genome' value='true' /> |
107 <param name='genome_size' value='10000'/> | 94 <param name='genome_size' value='10000' /> |
108 </conditional> | 95 </conditional> |
109 <param name='min_read_depth' value='30'/> | 96 <param name='min_read_depth' value='30' /> |
110 <param name='count' value='12'/> | 97 <param name='count' value='12' /> |
111 <output_collection name='subsamples_fastq' type='list' count='12'> | 98 <output_collection name='subsamples_fastq' type='list' count='12'> |
112 <element name='sample_01' file='sample_01_04.fastq' ftype='fastq'/> | 99 <element name='sample_01' file='sample_01_04.fastq' ftype='fastq' /> |
113 <element name='sample_02' file='sample_02_04.fastq' ftype='fastq'/> | 100 <element name='sample_02' file='sample_02_04.fastq' ftype='fastq' /> |
114 <element name='sample_03' file='sample_03_04.fastq' ftype='fastq'/> | 101 <element name='sample_03' file='sample_03_04.fastq' ftype='fastq' /> |
115 <element name='sample_04' file='sample_04_04.fastq' ftype='fastq'/> | 102 <element name='sample_04' file='sample_04_04.fastq' ftype='fastq' /> |
116 <element name='sample_05' file='sample_05_04.fastq' ftype='fastq'/> | 103 <element name='sample_05' file='sample_05_04.fastq' ftype='fastq' /> |
117 <element name='sample_06' file='sample_06_04.fastq' ftype='fastq'/> | 104 <element name='sample_06' file='sample_06_04.fastq' ftype='fastq' /> |
118 <element name='sample_07' file='sample_07_04.fastq' ftype='fastq'/> | 105 <element name='sample_07' file='sample_07_04.fastq' ftype='fastq' /> |
119 <element name='sample_08' file='sample_08_04.fastq' ftype='fastq'/> | 106 <element name='sample_08' file='sample_08_04.fastq' ftype='fastq' /> |
120 <element name='sample_09' file='sample_09_04.fastq' ftype='fastq'/> | 107 <element name='sample_09' file='sample_09_04.fastq' ftype='fastq' /> |
121 <element name='sample_10' file='sample_10_04.fastq' ftype='fastq'/> | 108 <element name='sample_10' file='sample_10_04.fastq' ftype='fastq' /> |
122 <element name='sample_11' file='sample_11_04.fastq' ftype='fastq'/> | 109 <element name='sample_11' file='sample_11_04.fastq' ftype='fastq' /> |
123 <element name='sample_12' file='sample_12_04.fastq' ftype='fastq'/> | 110 <element name='sample_12' file='sample_12_04.fastq' ftype='fastq' /> |
124 </output_collection> | 111 </output_collection> |
125 </test> | 112 </test> |
126 </tests> | 113 </tests> |
127 <help><![CDATA[ | 114 <help><![CDATA[ |
128 .. class:: infomark | 115 .. class:: infomark |
129 | 116 |
130 **Purpose** | 117 **Purpose** |
151 ---- | 138 ---- |
152 | 139 |
153 .. class:: infomark | 140 .. class:: infomark |
154 | 141 |
155 @PIPELINE@ | 142 @PIPELINE@ |
156 ]]></help> | 143 ]]> </help> |
157 <expand macro='citations'/> | 144 <expand macro='citations' /> |
158 </tool> | 145 </tool> |