Mercurial > repos > iuc > trycycler_partition
comparison trycycler_partition.xml @ 1:4688ae3b49b5 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 17:29:03 +0000 |
parents | 8fcec9049d68 |
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0:8fcec9049d68 | 1:4688ae3b49b5 |
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1 <tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='21.01'> | 1 <tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='20.01'> |
2 <description>assign the reads to the clusters</description> | 2 <description>assign the reads to the clusters</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 'partitions' | 10 mkdir -p 'partitions' |
11 #for $i in $input_cluster | 11 #for $i in $input_cluster |
12 #set $name = str($i.element_identifier) | 12 #set $name = str($i.element_identifier) |
25 #set $number = (str($name).split('_')[-1]).strip('.fasta') | 25 #set $number = (str($name).split('_')[-1]).strip('.fasta') |
26 #set $fullpath = '_'.join(['selected_cluster/cluster',str($number)]) | 26 #set $fullpath = '_'.join(['selected_cluster/cluster',str($number)]) |
27 mv '$fullpath/4_reads.fastq' 'partitions/partition_${number}.fastq' && | 27 mv '$fullpath/4_reads.fastq' 'partitions/partition_${number}.fastq' && |
28 #end for | 28 #end for |
29 echo 'bye!' | 29 echo 'bye!' |
30 ]]></command> | 30 ]]> </command> |
31 <inputs> | 31 <inputs> |
32 <param name='input_cluster' type='data' | 32 <param name='input_cluster' type='data' format='fasta' multiple='true' label='Cluster datasets' help='Clustered contigs (multiple FASTA files)' /> |
33 format='fasta' multiple='true' label='Cluster datasets' | 33 <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' /> |
34 help='Clustered contigs (multiple FASTA files)' /> | 34 <param argument='--min_aligned_len' type='integer' min='500' max='3500' value='1000' label='Min bases aligned' help='Reads with less than this many bases aligned (default = 1000) will be ignored.' /> |
35 <param name='reads' type='data' | 35 <param argument='--min_read_cov' type='integer' min='0' max='100' value='90' label='Min read length covered by alignments' help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' /> |
36 format='fastq,fastq.gz' label='Long-read datasets' | |
37 help='Long reads (FASTQ format) used to generate the assemblies' /> | |
38 <param argument='--min_aligned_len' type='integer' min='500' max='3500' | |
39 value='1000' label='Min bases aligned' | |
40 help='Reads with less than this many bases aligned (default = 1000) will be ignored.' /> | |
41 <param argument='--min_read_cov' type='integer' min='0' max='100' | |
42 value='90' label='Min read length covered by alignments' | |
43 help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' /> | |
44 </inputs> | 36 </inputs> |
45 <outputs> | 37 <outputs> |
46 <collection name='partitions' type='list' label='${tool.name} on ${on_string}'> | 38 <collection name='partitions' type='list' label='${tool.name} on ${on_string}'> |
47 <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions'/> | 39 <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions' /> |
48 </collection> | 40 </collection> |
49 </outputs> | 41 </outputs> |
50 <tests> | 42 <tests> |
51 <test> | 43 <test> |
52 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | 44 <param name='input_cluster' value='reconciled_cluster_01.fasta' /> |
53 <param name='reads' value='reads.fastq.gz'/> | 45 <param name='reads' value='reads.fastq.gz' /> |
54 <param name='min_aligned_len' value='1000'/> | 46 <param name='min_aligned_len' value='1000' /> |
55 <param name='min_read_cov' value='90'/> | 47 <param name='min_read_cov' value='90' /> |
56 <output_collection name='partitions' type='list' count='1'> | 48 <output_collection name='partitions' type='list' count='1'> |
57 <element name='partition_01' file='partition_01.fastq' ftype='fastq'/> | 49 <element name='partition_01' file='partition_01.fastq' ftype='fastq' /> |
58 </output_collection> | 50 </output_collection> |
59 </test> | 51 </test> |
60 <test> | 52 <test> |
61 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | 53 <param name='input_cluster' value='reconciled_cluster_01.fasta' /> |
62 <param name='reads' value='reads.fastq.gz'/> | 54 <param name='reads' value='reads.fastq.gz' /> |
63 <param name='min_aligned_len' value='1200'/> | 55 <param name='min_aligned_len' value='1200' /> |
64 <param name='min_read_cov' value='95'/> | 56 <param name='min_read_cov' value='95' /> |
65 <output_collection name='partitions' type='list' count='1'> | 57 <output_collection name='partitions' type='list' count='1'> |
66 <element name='partition_01' file='partition_02.fastq' ftype='fastq'/> | 58 <element name='partition_01' file='partition_02.fastq' ftype='fastq' /> |
67 </output_collection> | 59 </output_collection> |
68 </test> | 60 </test> |
69 <test> | 61 <test> |
70 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | 62 <param name='input_cluster' value='reconciled_cluster_01.fasta' /> |
71 <param name='reads' value='reads.fastq.gz'/> | 63 <param name='reads' value='reads.fastq.gz' /> |
72 <param name='min_aligned_len' value='900'/> | 64 <param name='min_aligned_len' value='900' /> |
73 <param name='min_read_cov' value='93'/> | 65 <param name='min_read_cov' value='93' /> |
74 <output_collection name='partitions' type='list' count='1'> | 66 <output_collection name='partitions' type='list' count='1'> |
75 <element name='partition_01' file='partition_03.fastq' ftype='fastq'/> | 67 <element name='partition_01' file='partition_03.fastq' ftype='fastq' /> |
76 </output_collection> | 68 </output_collection> |
77 </test> | 69 </test> |
78 <test> | 70 <test> |
79 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | 71 <param name='input_cluster' value='reconciled_cluster_01.fasta' /> |
80 <param name='reads' value='reads.fastq.gz'/> | 72 <param name='reads' value='reads.fastq.gz' /> |
81 <param name='min_aligned_len' value='1000'/> | 73 <param name='min_aligned_len' value='1000' /> |
82 <param name='min_read_cov' value='90'/> | 74 <param name='min_read_cov' value='90' /> |
83 <output_collection name='partitions' type='list' count='1'> | 75 <output_collection name='partitions' type='list' count='1'> |
84 <element name='partition_01' file='partition_04.fastq' ftype='fastq'/> | 76 <element name='partition_01' file='partition_04.fastq' ftype='fastq' /> |
85 </output_collection> | 77 </output_collection> |
86 </test> | 78 </test> |
87 </tests> | 79 </tests> |
88 <help><![CDATA[ | 80 <help><![CDATA[ |
89 | 81 |
113 ---- | 105 ---- |
114 | 106 |
115 .. class:: infomark | 107 .. class:: infomark |
116 | 108 |
117 @PIPELINE@ | 109 @PIPELINE@ |
118 ]]></help> | 110 ]]> </help> |
119 <expand macro='citations'/> | 111 <expand macro='citations' /> |
120 </tool> | 112 </tool> |