Mercurial > repos > iuc > trycycler_consensus

comparison trycycler_consensus.xml @ 1:e59bee4565b3 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 17:29:47 +0000
parents 93c6a7423090
children 9ded6109434a
comparison
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0:93c6a7423090 1:e59bee4565b3
1 <tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='21.01'> 1 <tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='20.01'>
2 <description>generate a consensus contig sequence for each cluster</description> 2 <description>generate a consensus contig sequence for each cluster</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 'selected_cluster' && 10 mkdir -p 'selected_cluster' &&
11 ln -s '${cluster_all_seqs}' 'selected_cluster/2_all_seqs.fasta' && 11 ln -s '${cluster_all_seqs}' 'selected_cluster/2_all_seqs.fasta' &&
12 ln -s '${reconcile_msa}' 'selected_cluster/3_msa.fasta' && 12 ln -s '${reconcile_msa}' 'selected_cluster/3_msa.fasta' &&
17 #end if 17 #end if
18 --min_aligned_len $min_aligned_len 18 --min_aligned_len $min_aligned_len
19 --min_read_cov $min_read_cov 19 --min_read_cov $min_read_cov
20 --threads \${GALAXY_SLOTS:-2} && 20 --threads \${GALAXY_SLOTS:-2} &&
21 mv 'selected_cluster/7_final_consensus.fasta' $consensus 21 mv 'selected_cluster/7_final_consensus.fasta' $consensus
22 ]]></command> 22 ]]> </command>
23 <inputs> 23 <inputs>
24 <param name='cluster_all_seqs' type='data' 24 <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' />
25 format='fasta' label='Reconciled cluster' 25 <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' />
26 help='Reconciled sequences file' /> 26 <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' />
27 <param name='reconcile_msa' type='data' 27 <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' />
28 format='fasta' label='Reconcile msa' 28 <param argument='--linear' type='boolean' truevalue='--linear' falsevalue='' label='Input contigs are not circular' help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
29 help='Multiple sequence alignment file' /> 29 <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.' />
30 <param name='partition_reads' type='data' 30 <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.' />
31 format='fastq' label='Partition reads'
32 help='Partitioned reads' />
33 <param name='reads' type='data'
34 format='fastq,fastq.gz' label='Long-read datasets'
35 help='Long reads (FASTQ format) used to generate the assemblies' />
36 <param argument='--linear' type='boolean'
37 truevalue='--linear' falsevalue=''
38 label='Input contigs are not circular'
39 help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
40 <param argument='--min_aligned_len' type='integer' min='500' max='3500'
41 value='1000' label='Min bases aligned'
42 help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />
43 <param argument='--min_read_cov' type='integer' min='0' max='100'
44 value='90' label='Min read length covered by alignments'
45 help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />
46 </inputs> 31 </inputs>
47 <outputs> 32 <outputs>
48 <data name='consensus' format='fasta' label='${tool.name} on ${on_string}'/> 33 <data name='consensus' format='fasta' label='${tool.name} on ${on_string}' />
49 </outputs> 34 </outputs>
50 <tests> 35 <tests>
51 <test> 36 <test>
52 <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta'/> 37 <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' />
53 <param name='reconcile_msa' value='aligned_cluster_01.fasta'/> 38 <param name='reconcile_msa' value='aligned_cluster_01.fasta' />
54 <param name='partition_reads' value='partition_01.fastq'/> 39 <param name='partition_reads' value='partition_01.fastq' />
55 <param name='reads' value='reads.fastq.gz'/> 40 <param name='reads' value='reads.fastq.gz' />
56 <param name='min_aligned_len' value='1200'/> 41 <param name='min_aligned_len' value='1200' />
57 <param name='min_read_cov' value='95'/> 42 <param name='min_read_cov' value='95' />
58 <output name='consensus' file='consensus_sequence_01.fasta'/> 43 <output name='consensus' file='consensus_sequence_01.fasta' />
59 </test> 44 </test>
60 <test> 45 <test>
61 <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta'/> 46 <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' />
62 <param name='reconcile_msa' value='aligned_cluster_02.fasta'/> 47 <param name='reconcile_msa' value='aligned_cluster_02.fasta' />
63 <param name='partition_reads' value='partition_01.fastq'/> 48 <param name='partition_reads' value='partition_01.fastq' />
64 <param name='reads' value='reads.fastq.gz'/> 49 <param name='reads' value='reads.fastq.gz' />
65 <param name='min_aligned_len' value='1100'/> 50 <param name='min_aligned_len' value='1100' />
66 <param name='min_read_cov' value='90'/> 51 <param name='min_read_cov' value='90' />
67 <output name='consensus' file='consensus_sequence_02.fasta'/> 52 <output name='consensus' file='consensus_sequence_02.fasta' />
68 </test> 53 </test>
69 <test> 54 <test>
70 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/> 55 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
71 <param name='reconcile_msa' value='aligned_cluster_03.fasta'/> 56 <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
72 <param name='partition_reads' value='partition_01.fastq'/> 57 <param name='partition_reads' value='partition_01.fastq' />
73 <param name='reads' value='reads.fastq.gz'/> 58 <param name='reads' value='reads.fastq.gz' />
74 <param name='min_aligned_len' value='1300'/> 59 <param name='min_aligned_len' value='1300' />
75 <param name='min_read_cov' value='97'/> 60 <param name='min_read_cov' value='97' />
76 <output name='consensus' file='consensus_sequence_03.fasta'/> 61 <output name='consensus' file='consensus_sequence_03.fasta' />
77 </test> 62 </test>
78 <test> 63 <test>
79 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/> 64 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
80 <param name='reconcile_msa' value='aligned_cluster_03.fasta'/> 65 <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
81 <param name='partition_reads' value='partition_01.fastq'/> 66 <param name='partition_reads' value='partition_01.fastq' />
82 <param name='reads' value='reads.fastq.gz'/> 67 <param name='reads' value='reads.fastq.gz' />
83 <param name='min_aligned_len' value='1000'/> 68 <param name='min_aligned_len' value='1000' />
84 <param name='min_read_cov' value='87'/> 69 <param name='min_read_cov' value='87' />
85 <output name='consensus' file='consensus_sequence_04.fasta'/> 70 <output name='consensus' file='consensus_sequence_04.fasta' />
86 </test> 71 </test>
87 </tests> 72 </tests>
88 <help><![CDATA[ 73 <help><![CDATA[
89 74
90 .. class:: infomark 75 .. class:: infomark
138 ---- 123 ----
139 124
140 .. class:: infomark 125 .. class:: infomark
141 126
142 @PIPELINE@ 127 @PIPELINE@
143 ]]></help> 128 ]]> </help>
144 <expand macro='citations'/> 129 <expand macro='citations' />
145 </tool> 130 </tool>