| Previous changeset 0:4ac81df20c74 (2021-02-11) Next changeset 2:937ea677d437 (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_reconcile_msa.xml |
| b |
| diff -r 4ac81df20c74 -r b64696992ee9 trycycler_reconcile_msa.xml --- a/trycycler_reconcile_msa.xml Thu Feb 11 19:26:05 2021 +0000 +++ b/trycycler_reconcile_msa.xml Sat Feb 13 17:31:16 2021 +0000 |
| [ |
| b'@@ -1,10 +1,10 @@\n-<tool id="trycycler_reconcile_msa" name="Trycycler reconcile/msa" version="@TOOL_VERSION@" profile="21.01">\n+<tool id="trycycler_reconcile_msa" name="Trycycler reconcile/msa" version="@TOOL_VERSION@" profile="20.01">\n <description>reconcile the contigs within each cluster and perform a multiple sequence alignment</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 #import re\n@@ -35,159 +35,122 @@\n --threads \\${GALAXY_SLOTS:-2} &&\n mv \'${fullpath}/2_all_seqs.fasta\' \'$reconciled_cluster\' &&\n mv \'${fullpath}/3_msa.fasta\' \'$aligned_cluster\'\n- ]]></command>\n+ ]]> </command>\n <inputs>\n- <param name="input_cluster" type="data" \n- format="fasta" label="Cluster multi-FASTA dataset" \n- help="The input should be an independent cluster generated by the *trycycler cluster* tool" />\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- <section name=\'initial_ckeck\'\n- title=\'Reconcile initial check options\'\n- expanded=\'true\'>\n- <param argument="--max_mash_dist" type="float" min="0" max="0.2" \n- value="0.02" label="Max Mash distance" \n- help="If any of the sequences have a pairwise Mash distance of more than this (default = 0.02), then the contigs will fail the initial check." />\n- <param argument="--max_length_diff" type="float" min="1" max="2" \n- value="1.1" label="Max relative length factor" \n- help="If any of the sequences have a pairwise relative length factor of more than this, then the contigs will fail the initial check. For example, if set to 1.1 (the default), then no contig can be more than 10% longer than any other." /> \n+ <param name="input_cluster" type="data" format="fasta" label="Cluster multi-FASTA dataset" help="The input should be an independent cluster generated by the *trycycler cluster* tool" />\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+ <section name=\'initial_ckeck\' title=\'Reconcile initial check options\' expanded=\'true\'>\n+ <param argument="--max_mash_dist" type="float" min="0" max="0.2" value="0.02" label="Max Mash distance" help="If any of the sequences have a pairwise Mash distance of more than this (default = 0.02), then the contigs will fail the initial check." />\n+ <param argument="--max_length_diff" type="float" min="1" max="2" value="1.1" label="Max relative length factor" help="If any of the sequences have a pairwise relative length factor of more than this, then the contigs will fail the initial check. For example, if set to 1.1 (the default), then no contig can be more than 10% longer than any other." />\n </section>\n- <section name="circularisation"\n- title="Reconcile circularization options"\n- expanded=\'true\'>\n- <pa'..b'n_identity" value="97" />\n </section>\n <section name="msa">\n- <param name="step" value="1100"/>\n- </section> \n- <output name=\'reconciled_cluster\' file=\'reconciled_cluster_03.fasta\'/>\n- <output name=\'aligned_cluster\' file=\'aligned_cluster_03.fasta\'/>\n+ <param name="step" value="1100" />\n+ </section>\n+ <output name=\'reconciled_cluster\' file=\'reconciled_cluster_03.fasta\' />\n+ <output name=\'aligned_cluster\' file=\'aligned_cluster_03.fasta\' />\n </test>\n <test>\n- <param name=\'input_cluster\' value=\'cluster_01.fasta\'/>\n- <param name="reads" value="reads.fastq.gz"/>\n+ <param name=\'input_cluster\' value=\'cluster_01.fasta\' />\n+ <param name="reads" value="reads.fastq.gz" />\n <section name="initial_check">\n- <param name="max_length_diff" value="1.2"/>\n+ <param name="max_length_diff" value="1.2" />\n </section>\n <section name="circularisation">\n- <param name="max_add_seq" value="920"/>\n- <param name="max_trim_seq_percent" value="12"/>\n+ <param name="max_add_seq" value="920" />\n+ <param name="max_trim_seq_percent" value="12" />\n </section>\n <section name="final_check">\n- <param name="min_identity" value="95"/>\n- <param name="max_indel_size" value="230"/>\n+ <param name="min_identity" value="95" />\n+ <param name="max_indel_size" value="230" />\n </section>\n <section name="msa">\n- <param name="kmer" value="33"/>\n- </section> \n- <output name=\'reconciled_cluster\' file=\'reconciled_cluster_04.fasta\'/>\n- <output name=\'aligned_cluster\' file=\'aligned_cluster_04.fasta\'/>\n+ <param name="kmer" value="33" />\n+ </section>\n+ <output name=\'reconciled_cluster\' file=\'reconciled_cluster_04.fasta\' />\n+ <output name=\'aligned_cluster\' file=\'aligned_cluster_04.fasta\' />\n </test>\n <test>\n- <param name=\'input_cluster\' value=\'cluster_01.fasta\'/>\n- <param name="reads" value="reads.fastq.gz"/>\n+ <param name=\'input_cluster\' value=\'cluster_01.fasta\' />\n+ <param name="reads" value="reads.fastq.gz" />\n <section name="initial_check">\n- <param name="max_mash_dist" value="0.3"/>\n+ <param name="max_mash_dist" value="0.3" />\n </section>\n <section name="circularisation">\n- <param name="max_add_seq_percentage" value="8"/>\n- <param name="max_trim_seq" value="45300"/>\n+ <param name="max_add_seq_percentage" value="8" />\n+ <param name="max_trim_seq" value="45300" />\n </section>\n <section name="final_check">\n- <param name="min_identity" value="97"/>\n+ <param name="min_identity" value="97" />\n </section>\n <section name="msa">\n- <param name="step" value="1100"/>\n- <param name="lookahead" value="980"/>\n- </section> \n- <output name=\'reconciled_cluster\' file=\'reconciled_cluster_05.fasta\'/>\n- <output name=\'aligned_cluster\' file=\'aligned_cluster_05.fasta\'/>\n+ <param name="step" value="1100" />\n+ <param name="lookahead" value="980" />\n+ </section>\n+ <output name=\'reconciled_cluster\' file=\'reconciled_cluster_05.fasta\' />\n+ <output name=\'aligned_cluster\' file=\'aligned_cluster_05.fasta\' />\n </test>\n- \n+\n </tests>\n <help><![CDATA[\n \n@@ -250,6 +213,6 @@\n .. class:: infomark\n \n @PIPELINE@\n- ]]></help>\n- <expand macro=\'citations\'/>\n+ ]]> </help>\n+ <expand macro=\'citations\' />\n </tool>\n' |