Mercurial > repos > iuc > trycycler_partition
changeset 1:4688ae3b49b5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
| author | iuc |
|---|---|
| date | Sat, 13 Feb 2021 17:29:03 +0000 |
| parents | 8fcec9049d68 |
| children | ebd801e712bc |
| files | trycycler_partition.xml |
| diffstat | 1 files changed, 31 insertions(+), 39 deletions(-) [+] |
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--- a/trycycler_partition.xml Thu Feb 11 19:23:50 2021 +0000 +++ b/trycycler_partition.xml Sat Feb 13 17:29:03 2021 +0000 @@ -1,10 +1,10 @@ -<tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='21.01'> +<tool id='trycycler_partition' name='Trycycler partition' version='@TOOL_VERSION@' profile='20.01'> <description>assign the reads to the clusters</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 'partitions' @@ -27,61 +27,53 @@ mv '$fullpath/4_reads.fastq' 'partitions/partition_${number}.fastq' && #end for echo 'bye!' - ]]></command> + ]]> </command> <inputs> - <param name='input_cluster' type='data' - format='fasta' multiple='true' label='Cluster datasets' - help='Clustered contigs (multiple FASTA files)' /> - <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='--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='input_cluster' type='data' format='fasta' multiple='true' label='Cluster datasets' help='Clustered contigs (multiple FASTA files)' /> + <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='--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> <collection name='partitions' type='list' label='${tool.name} on ${on_string}'> - <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions'/> + <discover_datasets pattern='__designation_and_ext__' format='fastq' directory='partitions' /> </collection> </outputs> <tests> <test> - <param name='input_cluster' value='reconciled_cluster_01.fasta'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_aligned_len' value='1000'/> - <param name='min_read_cov' value='90'/> + <param name='input_cluster' value='reconciled_cluster_01.fasta' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_aligned_len' value='1000' /> + <param name='min_read_cov' value='90' /> <output_collection name='partitions' type='list' count='1'> - <element name='partition_01' file='partition_01.fastq' ftype='fastq'/> + <element name='partition_01' file='partition_01.fastq' ftype='fastq' /> </output_collection> </test> <test> - <param name='input_cluster' value='reconciled_cluster_01.fasta'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_aligned_len' value='1200'/> - <param name='min_read_cov' value='95'/> + <param name='input_cluster' value='reconciled_cluster_01.fasta' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_aligned_len' value='1200' /> + <param name='min_read_cov' value='95' /> <output_collection name='partitions' type='list' count='1'> - <element name='partition_01' file='partition_02.fastq' ftype='fastq'/> + <element name='partition_01' file='partition_02.fastq' ftype='fastq' /> </output_collection> </test> <test> - <param name='input_cluster' value='reconciled_cluster_01.fasta'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_aligned_len' value='900'/> - <param name='min_read_cov' value='93'/> + <param name='input_cluster' value='reconciled_cluster_01.fasta' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_aligned_len' value='900' /> + <param name='min_read_cov' value='93' /> <output_collection name='partitions' type='list' count='1'> - <element name='partition_01' file='partition_03.fastq' ftype='fastq'/> + <element name='partition_01' file='partition_03.fastq' ftype='fastq' /> </output_collection> </test> <test> - <param name='input_cluster' value='reconciled_cluster_01.fasta'/> - <param name='reads' value='reads.fastq.gz'/> - <param name='min_aligned_len' value='1000'/> - <param name='min_read_cov' value='90'/> + <param name='input_cluster' value='reconciled_cluster_01.fasta' /> + <param name='reads' value='reads.fastq.gz' /> + <param name='min_aligned_len' value='1000' /> + <param name='min_read_cov' value='90' /> <output_collection name='partitions' type='list' count='1'> - <element name='partition_01' file='partition_04.fastq' ftype='fastq'/> + <element name='partition_01' file='partition_04.fastq' ftype='fastq' /> </output_collection> </test> </tests> @@ -115,6 +107,6 @@ .. class:: infomark @PIPELINE@ - ]]></help> - <expand macro='citations'/> + ]]> </help> + <expand macro='citations' /> </tool>