Mercurial > repos > iuc > trycycler_consensus

comparison trycycler_consensus.xml @ 5:9ded6109434a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 7352940deeeddc0f1b7f0ac90451c4aa19df75b4"
author iuc
date Sat, 18 Dec 2021 19:50:44 +0000
parents e59bee4565b3
children
comparison
equal deleted inserted replaced
4:43af166bc01e 5:9ded6109434a
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' &&
13 ln -s '${partition_reads}' 'selected_cluster/4_reads.fastq' && 13 ln -s '${partition_reads}' 'selected_cluster/4_reads.fastq' &&
14 trycycler consensus --cluster_dir 'selected_cluster' 14 trycycler consensus --cluster_dir 'selected_cluster'
15 #if $linear 15 $linear
16 --linear
17 #end if
18 --min_aligned_len $min_aligned_len 16 --min_aligned_len $min_aligned_len
19 --min_read_cov $min_read_cov 17 --min_read_cov $min_read_cov
20 --threads \${GALAXY_SLOTS:-2} && 18 --threads \${GALAXY_SLOTS:-2} &&
21 mv 'selected_cluster/7_final_consensus.fasta' $consensus 19 mv 'selected_cluster/7_final_consensus.fasta' $consensus
22 ]]> </command> 20 ]]> </command>
23 <inputs> 21 <inputs>
24 <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' /> 22 <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' />
25 <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' /> 23 <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' />
26 <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' /> 24 <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' />
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 <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.' /> 25 <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 <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.' /> 26 <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 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.' /> 27 <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 </inputs> 28 </inputs>
32 <outputs> 29 <outputs>
35 <tests> 32 <tests>
36 <test> 33 <test>
37 <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' /> 34 <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' />
38 <param name='reconcile_msa' value='aligned_cluster_01.fasta' /> 35 <param name='reconcile_msa' value='aligned_cluster_01.fasta' />
39 <param name='partition_reads' value='partition_01.fastq' /> 36 <param name='partition_reads' value='partition_01.fastq' />
40 <param name='reads' value='reads.fastq.gz' />
41 <param name='min_aligned_len' value='1200' /> 37 <param name='min_aligned_len' value='1200' />
42 <param name='min_read_cov' value='95' /> 38 <param name='min_read_cov' value='95' />
43 <output name='consensus' file='consensus_sequence_01.fasta' /> 39 <output name='consensus' file='consensus_sequence_01.fasta' />
44 </test> 40 </test>
45 <test> 41 <test>
46 <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' /> 42 <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' />
47 <param name='reconcile_msa' value='aligned_cluster_02.fasta' /> 43 <param name='reconcile_msa' value='aligned_cluster_02.fasta' />
48 <param name='partition_reads' value='partition_01.fastq' /> 44 <param name='partition_reads' value='partition_01.fastq' />
49 <param name='reads' value='reads.fastq.gz' />
50 <param name='min_aligned_len' value='1100' /> 45 <param name='min_aligned_len' value='1100' />
51 <param name='min_read_cov' value='90' /> 46 <param name='min_read_cov' value='90' />
52 <output name='consensus' file='consensus_sequence_02.fasta' /> 47 <output name='consensus' file='consensus_sequence_02.fasta' />
53 </test> 48 </test>
54 <test> 49 <test>
55 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' /> 50 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
56 <param name='reconcile_msa' value='aligned_cluster_03.fasta' /> 51 <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
57 <param name='partition_reads' value='partition_01.fastq' /> 52 <param name='partition_reads' value='partition_01.fastq' />
58 <param name='reads' value='reads.fastq.gz' />
59 <param name='min_aligned_len' value='1300' /> 53 <param name='min_aligned_len' value='1300' />
60 <param name='min_read_cov' value='97' /> 54 <param name='min_read_cov' value='97' />
61 <output name='consensus' file='consensus_sequence_03.fasta' /> 55 <output name='consensus' file='consensus_sequence_03.fasta' />
62 </test> 56 </test>
63 <test> 57 <test>
64 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' /> 58 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
65 <param name='reconcile_msa' value='aligned_cluster_03.fasta' /> 59 <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
66 <param name='partition_reads' value='partition_01.fastq' /> 60 <param name='partition_reads' value='partition_01.fastq' />
67 <param name='reads' value='reads.fastq.gz' />
68 <param name='min_aligned_len' value='1000' /> 61 <param name='min_aligned_len' value='1000' />
69 <param name='min_read_cov' value='87' /> 62 <param name='min_read_cov' value='87' />
70 <output name='consensus' file='consensus_sequence_04.fasta' /> 63 <output name='consensus' file='consensus_sequence_04.fasta' />
71 </test> 64 </test>
72 </tests> 65 </tests>