Mercurial > repos > iuc > trycycler_partition

comparison trycycler_partition.xml @ 1:e5956fe0f881 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 17:24:08 +0000
parents 6a80be58a760
children
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0:6a80be58a760 1:e5956fe0f881
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>