Mercurial > repos > iuc > trycycler_consensus
changeset 5:9ded6109434a draft
"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 | 43af166bc01e |
| children | 19bdfd1e6fe3 |
| files | trycycler_consensus.xml |
| diffstat | 1 files changed, 1 insertions(+), 8 deletions(-) [+] |
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--- a/trycycler_consensus.xml Mon Dec 13 21:17:36 2021 +0000 +++ b/trycycler_consensus.xml Sat Dec 18 19:50:44 2021 +0000 @@ -12,9 +12,7 @@ ln -s '${reconcile_msa}' 'selected_cluster/3_msa.fasta' && ln -s '${partition_reads}' 'selected_cluster/4_reads.fastq' && trycycler consensus --cluster_dir 'selected_cluster' - #if $linear - --linear - #end if + $linear --min_aligned_len $min_aligned_len --min_read_cov $min_read_cov --threads \${GALAXY_SLOTS:-2} && @@ -24,7 +22,6 @@ <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' /> <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' /> <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' /> - <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' /> <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.' /> <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.' /> <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.' /> @@ -37,7 +34,6 @@ <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' /> <param name='reconcile_msa' value='aligned_cluster_01.fasta' /> <param name='partition_reads' value='partition_01.fastq' /> - <param name='reads' value='reads.fastq.gz' /> <param name='min_aligned_len' value='1200' /> <param name='min_read_cov' value='95' /> <output name='consensus' file='consensus_sequence_01.fasta' /> @@ -46,7 +42,6 @@ <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' /> <param name='reconcile_msa' value='aligned_cluster_02.fasta' /> <param name='partition_reads' value='partition_01.fastq' /> - <param name='reads' value='reads.fastq.gz' /> <param name='min_aligned_len' value='1100' /> <param name='min_read_cov' value='90' /> <output name='consensus' file='consensus_sequence_02.fasta' /> @@ -55,7 +50,6 @@ <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' /> <param name='reconcile_msa' value='aligned_cluster_03.fasta' /> <param name='partition_reads' value='partition_01.fastq' /> - <param name='reads' value='reads.fastq.gz' /> <param name='min_aligned_len' value='1300' /> <param name='min_read_cov' value='97' /> <output name='consensus' file='consensus_sequence_03.fasta' /> @@ -64,7 +58,6 @@ <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' /> <param name='reconcile_msa' value='aligned_cluster_03.fasta' /> <param name='partition_reads' value='partition_01.fastq' /> - <param name='reads' value='reads.fastq.gz' /> <param name='min_aligned_len' value='1000' /> <param name='min_read_cov' value='87' /> <output name='consensus' file='consensus_sequence_04.fasta' />