| Previous changeset 0:93c6a7423090 (2021-02-11) Next changeset 2:356afed970b4 (2021-10-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912" |
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modified:
trycycler_consensus.xml |
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| diff -r 93c6a7423090 -r e59bee4565b3 trycycler_consensus.xml --- a/trycycler_consensus.xml Thu Feb 11 19:24:35 2021 +0000 +++ b/trycycler_consensus.xml Sat Feb 13 17:29:47 2021 +0000 |
| [ |
| b"@@ -1,10 +1,10 @@\n-<tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='21.01'>\n+<tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='20.01'>\n <description>generate a consensus contig sequence for each cluster</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro='edam_ontology'/>\n- <expand macro='requirements'/>\n+ <expand macro='edam_ontology' />\n+ <expand macro='requirements' />\n <version_command>trycycler --version</version_command>\n <command detect_errors='exit_code'><![CDATA[\n mkdir -p 'selected_cluster' &&\n@@ -19,70 +19,55 @@\n --min_read_cov $min_read_cov\n --threads \\${GALAXY_SLOTS:-2} &&\n mv 'selected_cluster/7_final_consensus.fasta' $consensus\n- ]]></command>\n+ ]]> </command>\n <inputs>\n- <param name='cluster_all_seqs' type='data' \n- format='fasta' label='Reconciled cluster' \n- help='Reconciled sequences file' />\n- <param name='reconcile_msa' type='data' \n- format='fasta' label='Reconcile msa' \n- help='Multiple sequence alignment file' />\n- <param name='partition_reads' type='data' \n- format='fastq' label='Partition reads' \n- help='Partitioned reads' />\n- <param name='reads' type='data' \n- format='fastq,fastq.gz' label='Long-read datasets' \n- help='Long reads (FASTQ format) used to generate the assemblies' />\n- <param argument='--linear' type='boolean' \n- truevalue='--linear' falsevalue='' \n- label='Input contigs are not circular' \n- help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />\n- <param argument='--min_aligned_len' type='integer' min='500' max='3500' \n- value='1000' label='Min bases aligned' \n- help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />\n- <param argument='--min_read_cov' type='integer' min='0' max='100' \n- value='90' label='Min read length covered by alignments' \n- help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />\n+ <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' />\n+ <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' />\n+ <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' />\n+ <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' />\n+ <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.' />\n+ <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.' />\n+ <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.' />\n </inputs>\n <outputs>\n- <data name='consensus' format='fasta' label='${tool.name} on ${on_string}'/>\n+ <data name='consensus' format='fasta' label='${tool.name} on ${on_string}' />\n </outputs>\n <tests>\n <test>\n- <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta'/>\n- <param name="..b"luster_01.fasta'/>\n- <param name='partition_reads' value='partition_01.fastq'/>\n- <param name='reads' value='reads.fastq.gz'/>\n- <param name='min_aligned_len' value='1200'/>\n- <param name='min_read_cov' value='95'/>\n- <output name='consensus' file='consensus_sequence_01.fasta'/>\n+ <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' />\n+ <param name='reconcile_msa' value='aligned_cluster_01.fasta' />\n+ <param name='partition_reads' value='partition_01.fastq' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_aligned_len' value='1200' />\n+ <param name='min_read_cov' value='95' />\n+ <output name='consensus' file='consensus_sequence_01.fasta' />\n </test>\n <test>\n- <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta'/>\n- <param name='reconcile_msa' value='aligned_cluster_02.fasta'/>\n- <param name='partition_reads' value='partition_01.fastq'/>\n- <param name='reads' value='reads.fastq.gz'/>\n- <param name='min_aligned_len' value='1100'/>\n- <param name='min_read_cov' value='90'/>\n- <output name='consensus' file='consensus_sequence_02.fasta'/>\n+ <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' />\n+ <param name='reconcile_msa' value='aligned_cluster_02.fasta' />\n+ <param name='partition_reads' value='partition_01.fastq' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_aligned_len' value='1100' />\n+ <param name='min_read_cov' value='90' />\n+ <output name='consensus' file='consensus_sequence_02.fasta' />\n </test>\n <test>\n- <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/>\n- <param name='reconcile_msa' value='aligned_cluster_03.fasta'/>\n- <param name='partition_reads' value='partition_01.fastq'/>\n- <param name='reads' value='reads.fastq.gz'/>\n- <param name='min_aligned_len' value='1300'/>\n- <param name='min_read_cov' value='97'/>\n- <output name='consensus' file='consensus_sequence_03.fasta'/>\n+ <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />\n+ <param name='reconcile_msa' value='aligned_cluster_03.fasta' />\n+ <param name='partition_reads' value='partition_01.fastq' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_aligned_len' value='1300' />\n+ <param name='min_read_cov' value='97' />\n+ <output name='consensus' file='consensus_sequence_03.fasta' />\n </test>\n <test>\n- <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta'/>\n- <param name='reconcile_msa' value='aligned_cluster_03.fasta'/>\n- <param name='partition_reads' value='partition_01.fastq'/>\n- <param name='reads' value='reads.fastq.gz'/>\n- <param name='min_aligned_len' value='1000'/>\n- <param name='min_read_cov' value='87'/>\n- <output name='consensus' file='consensus_sequence_04.fasta'/>\n+ <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />\n+ <param name='reconcile_msa' value='aligned_cluster_03.fasta' />\n+ <param name='partition_reads' value='partition_01.fastq' />\n+ <param name='reads' value='reads.fastq.gz' />\n+ <param name='min_aligned_len' value='1000' />\n+ <param name='min_read_cov' value='87' />\n+ <output name='consensus' file='consensus_sequence_04.fasta' />\n </test>\n </tests>\n <help><![CDATA[\n@@ -140,6 +125,6 @@\n .. class:: infomark\n \n @PIPELINE@\n- ]]></help>\n- <expand macro='citations'/>\n+ ]]> </help>\n+ <expand macro='citations' />\n </tool>\n" |