Mercurial > repos > iuc > trycycler_partition
comparison trycycler_partition.xml @ 0:8fcec9049d68 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
author | iuc |
---|---|
date | Thu, 11 Feb 2021 19:23:50 +0000 |
parents | |
children | 4688ae3b49b5 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:8fcec9049d68 |
---|---|
1 <tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='21.01'> | |
2 <description>assign the reads to the clusters</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro='edam_ontology'/> | |
7 <expand macro='requirements'/> | |
8 <version_command>trycycler --version</version_command> | |
9 <command detect_errors='exit_code'><![CDATA[ | |
10 mkdir -p 'partitions' | |
11 #for $i in $input_cluster | |
12 #set $name = str($i.element_identifier) | |
13 #set $number = (str($name).split('_')[-1]).strip('.fasta') | |
14 #set $fullpath = '_'.join(['selected_cluster/cluster',str($number)]) | |
15 mkdir -p $fullpath/ && | |
16 ln -s '${i}' '$fullpath/2_all_seqs.fasta' && | |
17 #end for | |
18 trycycler partition --cluster_dir 'selected_cluster'/cluster_* | |
19 --reads '$reads' | |
20 --min_aligned_len $min_aligned_len | |
21 --min_read_cov $min_read_cov | |
22 --threads \${GALAXY_SLOTS:-2} && | |
23 #for $i in $input_cluster | |
24 #set $name = str($i.element_identifier) | |
25 #set $number = (str($name).split('_')[-1]).strip('.fasta') | |
26 #set $fullpath = '_'.join(['selected_cluster/cluster',str($number)]) | |
27 mv '$fullpath/4_reads.fastq' 'partitions/partition_${number}.fastq' && | |
28 #end for | |
29 echo 'bye!' | |
30 ]]></command> | |
31 <inputs> | |
32 <param name='input_cluster' type='data' | |
33 format='fasta' multiple='true' label='Cluster datasets' | |
34 help='Clustered contigs (multiple FASTA files)' /> | |
35 <param name='reads' type='data' | |
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> | |
45 <outputs> | |
46 <collection name='partitions' type='list' label='${tool.name} on ${on_string}'> | |
47 <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions'/> | |
48 </collection> | |
49 </outputs> | |
50 <tests> | |
51 <test> | |
52 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | |
53 <param name='reads' value='reads.fastq.gz'/> | |
54 <param name='min_aligned_len' value='1000'/> | |
55 <param name='min_read_cov' value='90'/> | |
56 <output_collection name='partitions' type='list' count='1'> | |
57 <element name='partition_01' file='partition_01.fastq' ftype='fastq'/> | |
58 </output_collection> | |
59 </test> | |
60 <test> | |
61 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | |
62 <param name='reads' value='reads.fastq.gz'/> | |
63 <param name='min_aligned_len' value='1200'/> | |
64 <param name='min_read_cov' value='95'/> | |
65 <output_collection name='partitions' type='list' count='1'> | |
66 <element name='partition_01' file='partition_02.fastq' ftype='fastq'/> | |
67 </output_collection> | |
68 </test> | |
69 <test> | |
70 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | |
71 <param name='reads' value='reads.fastq.gz'/> | |
72 <param name='min_aligned_len' value='900'/> | |
73 <param name='min_read_cov' value='93'/> | |
74 <output_collection name='partitions' type='list' count='1'> | |
75 <element name='partition_01' file='partition_03.fastq' ftype='fastq'/> | |
76 </output_collection> | |
77 </test> | |
78 <test> | |
79 <param name='input_cluster' value='reconciled_cluster_01.fasta'/> | |
80 <param name='reads' value='reads.fastq.gz'/> | |
81 <param name='min_aligned_len' value='1000'/> | |
82 <param name='min_read_cov' value='90'/> | |
83 <output_collection name='partitions' type='list' count='1'> | |
84 <element name='partition_01' file='partition_04.fastq' ftype='fastq'/> | |
85 </output_collection> | |
86 </test> | |
87 </tests> | |
88 <help><![CDATA[ | |
89 | |
90 .. class:: infomark | |
91 | |
92 **Purpose** | |
93 | |
94 The *Trycycler partition* split the reads between the different clusters, i.e. each read will be assigned to whichever cluster it best aligns and saved into a file for that cluster. This step is run once for your entire genome (i.e. not on a per-cluster basis). | |
95 | |
96 ---- | |
97 | |
98 .. class:: infomark | |
99 | |
100 **Input** | |
101 | |
102 This tool requires as input the set of clustered considered valuable, and the long-read dataset used previously. | |
103 | |
104 ---- | |
105 | |
106 .. class:: infomark | |
107 | |
108 **Output** | |
109 | |
110 After **Trycycler partition** completes, if will generate a file per cluster, each of which contains its share of the total reads. | |
111 | |
112 | |
113 ---- | |
114 | |
115 .. class:: infomark | |
116 | |
117 @PIPELINE@ | |
118 ]]></help> | |
119 <expand macro='citations'/> | |
120 </tool> |