Mercurial > repos > iuc > trycycler_consensus
changeset 1:e59bee4565b3 draft
"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 | 356afed970b4 |
| files | trycycler_consensus.xml |
| diffstat | 1 files changed, 42 insertions(+), 57 deletions(-) [+] |
line wrap: on
line diff
--- a/trycycler_consensus.xml Thu Feb 11 19:24:35 2021 +0000 +++ b/trycycler_consensus.xml Sat Feb 13 17:29:47 2021 +0000 @@ -1,10 +1,10 @@ -<tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='21.01'> +<tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='20.01'> <description>generate a consensus contig sequence for each cluster</description> <macros> <import>macros.xml</import> </macros> - <expand macro='edam_ontology'/> - <expand macro='requirements'/> + <expand macro='edam_ontology' /> + <expand macro='requirements' /> <version_command>trycycler --version</version_command> <command detect_errors='exit_code'><![CDATA[ mkdir -p 'selected_cluster' && @@ -19,70 +19,55 @@ --min_read_cov $min_read_cov --threads \${GALAXY_SLOTS:-2} && mv 'selected_cluster/7_final_consensus.fasta' $consensus - ]]></command> + ]]> </command> <inputs> - <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.' /> + <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.' /> </inputs> <outputs> - <data name='consensus' format='fasta' label='${tool.name} on ${on_string}'/> + <data name='consensus' format='fasta' label='${tool.name} on ${on_string}' /> </outputs> <tests> <test> - <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'/> + <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' /> </test> <test> - <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'/> + <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' /> </test> <test> - <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'/> + <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' /> </test> <test> - <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'/> + <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' /> </test> </tests> <help><![CDATA[ @@ -140,6 +125,6 @@ .. class:: infomark @PIPELINE@ - ]]></help> - <expand macro='citations'/> + ]]> </help> + <expand macro='citations' /> </tool>