| Previous changeset 4:59bd28f6265d (2021-12-13) Next changeset 6:bb11fefb23a3 (2024-04-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 6f7d090f3c68336bace91ab1fe4f9c1163d943db |
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modified:
macros.xml trycycler_reconcile_msa.xml |
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added:
test-data/cluster_01 |
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| diff -r 59bd28f6265d -r cb1e3db43020 macros.xml --- a/macros.xml Mon Dec 13 21:16:05 2021 +0000 +++ b/macros.xml Wed Mar 29 20:24:48 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.5.3</token> + <token name="@TOOL_VERSION@">0.5.4</token> <token name="@PIPELINE@"> **Trycycler pipeline** |
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| diff -r 59bd28f6265d -r cb1e3db43020 test-data/cluster_01 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_01 Wed Mar 29 20:24:48 2023 +0000 |
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| b'@@ -0,0 +1,8 @@\n+>C_contig_2\n+CTCCCCAACCAAACTCTACAAAAAGAGTTTCAATCGATCCCCTATAAATCCGCATATATTTTGGCCGCTAGAAAAGGCGATTTAAAAACCAAGGTCGATGTGATAGGGAAAGTATGTGGAATGTCGAACTCATCGGCGATAAGGGTGTTGGATCAATTTCTTCCTTCATCTAGAAACAAAGACGTTAGAGAAACGATAGATAAGTCTGATTCAGAGAAGAATCGCCAATTATCTGATTTCTTAATAGAGATACTTCGCATCATATGTTCCGGAGTTTCTTTGTCCTCCTATAACGAAAATCTTCTACAACAGCTTTTTGAACTTTTTAAGCAAAAGAGCTGATCCTCCGTCAGCTCATATATATATTTATTATATATATATTTATTTAGGGATTTGATTTTACGAGAGAGATTTGCAACTCTTGGTGGTAGACTTTGCAACTCTTGGTGGTAGACTTTGCAACTCTTGGTGGTAGACTTTGCAACTCTTGGTGGTAGGGTGGTAGACTTGGTCATAATGGACTTTTGTTAAAAAATTTCTTAAAATCTTAGAGCTCCGATTTTGAATAGCTTTGGTTAAGAAAATGGGCTCGATGGCTTTCCATAAAAGTAGATTGTTCTTAACTTTTGGGGACGCGTCGGAAATTTGGTTATCTACTTTATCTCATCTAACTAGAAAAAATTATGCGTCTGGGATTAACTTTCTTGTTTCTTTAGAGATTCTGGATTTATCGGAAACCTTGATAAAGGCTATTTCTCTTGACCACAGCGAATCTTTGTTTAAAATCAAGTCTCTAGATGTTTTTAATGGAAAAGTCGTTTCAGAGGCCTCTAAACAGGCTAGAGCGGCATGCTACATATCTTTCACAAAGTTTTTGTATAGATTGACCAAGGGATATATTAAACCCGCTATTCCATTGAAAGATTTTGGAAACACTACATTTTTTAAAATCCGAGACAAAATCAAAACAGAATCGATTTCTAAGCAGGAATGGACAGTTTTTTTTGAAGCGCTCCGGATAGTGAATTATAGAGACTATTTAATCGGTAAATTGATTGTACAAGGGATCCGTAAGTTAGACGAAATTTTGTCTTTGCGCACAGACGATCTATTTTTTGCATCCAATCAGATTTCCTTTCGCATTAAAAAAAGACAGAATAAAGAAACCAAAATTCTAATCACATTTCCTATCAGCTTAATGGAAGAGTTGCAAAAATACACTTGTGGGAGAAATGGGAGAGTATTTGTTTCTAAAATAGGGATTCCTGTAACAACAAGTCAGGTTGCGCATAATTTTAGGCTTGCAGAGTTCCATAGTGCTATGAAAATAAAAATTACTCCCAGAGTACTTCGTGCAAGCGCTTTGATTCATTTAAAGCAAATAGGATTAAAAGATGAGGAAATCATGCGTATTTCCTGTCTCTCATCGAGACAAAGTGTGTGTTCTTATTGTTCTGGGGAAGAGGTAAGTCCTCTAGTACAAACACCCACAATATTGTGATATAATTAAAATTATATTCATATTCTGTTGCCAGAAAAAACACCTTTAGGCTATATTAGAGCCATCTTCTTTGAAGCATTGTCTTCTCGAGAGGATTTATCGTACGCAAATATCATCTTTGCGGTTGCGTGTCCCGTGACCTTCATTATGTCGGAGTCTGAGCACCCTAGGCGTTTGTACTCCGTCACAGCGGTTGCTCGAAGCACGTGCGGGGTTATCTTAAAAGGGATTGCAGCTTGTAGTCCTGCTTGAGAGAACGTGCGGGCGATTTGCCTTAACCCCACCATTTTTCCGGAGCGAGTTACGAAGACAGAAAACCTCTTCGTTGACCGATGTACTCTTGTAGAAAGTGCATAAACTTCTGAGGATAAGTTATAATAATCCTCTTTTCTGTCTGACGGTTCTTAAGCTGGGAGAAAGAAATGGTAGCTTGTTGGAAACAAATCTGACTAATCTCCAAGCTTAAGACTTCAGAGGAGCGTTTACCTCCTTGGAGCATTGTCTGGGCGATCAACCAATCCCGGGCGTTGATTTTTTTTAGCTCTTTTAGGAAGGATGCTGTTTGCAAACTGTTCATCGCATCCGTTTTTACTATTTCCCTGGTTTTAAAAAATGTTCGACTATTTTCTTGTTTAGAAGGTTGCGCTATAGCGACTATTCCTTGAGTCATCCTGTTTAGGAATCTTGTTAAGGAAATATAGCTTGCTGCTCGAACTTGTTTAGTACCTTCGGTCCAAGAAGTCTTGGCAGAGGAAACTTTTTTAATCGCATCTAGGATTAGATTATGATTTAAAAGGGAAAACTCTTGCAGATTCATATCCAAAGACAATAGACCAATCTTTTCTAAAGACAAAAAAGATCCTCGATATGATCTACAAGTATGTTTGTTGAGTGATGCGGTCCAATGCATAATAACTTCGAATAAGGAGAAGCTTTTCATGCGTTTCCAATAGGATTCTTGGCGAATTTTTAAAACTTCCTGATAAGACTTTTCGCTATATTCTAACGACATTTCTTGCTGCAAAGATAAAATCCCTTTACCCATGAAATCCCTCGTGATATAACCTATCCGCAAAATGTCCTGATTAGTGAAATAATCAGGTTGTTAACAGGATAGCACGCTCGGTATTTTTTTATATAAACATGAAAACTCGTTCCGAAATAGAAAATCGCATGCAAGATATCGAGTATGCGTTGTTAGGTAAAGCTCTGATATTTGAAGACTCTACTGAGTATATTCTGAGGCAGCTTGCTAATTATGAGTTTAAGTGTTCCCATCATAAAAACATATTCATAGTATTTAAATACTTAAAAGACAATGGATTACCTATAACTGTAGACTCGGCTTGGGAAGAGCTTTTGCGGCGTCGTATCAAAGATATGGACAAATCGTATCTCGGGTTAATGTTGCATGATGCTTTATCAAATGACAAGCTTAGATCCGTTTCTCATACGGTTTTCCTCGATGATTTGAGCGTGTGTAGCGCTGAAGAAAATTTGAGCAATTTCATTTTCCGCTCGTTTAATGAGTACAATGAAAATCCATTGCGTAGATCTCCGTTTCTATTGCTTGAGCGTATAAAGGGAAGGCTTGATAGTGCTATAGCAAAGACTTTTTCTATTCGCAGCGCTAGAGGCCGGTCTATTTATGATATATTCTCACAGTCAGAAATTGGAGTGCTGGCTCGTATAAAAAAAAGACGAGCAGCGTTCTCTGAGAATCAAAATTCTTTCTTTGATGGCTTCCCAACAGGATACAAGGATATTGATGATAAAGGAGTTATCTTAGCTAAAGGTAATTTCGTGATTATAGCAGCTAGGCCATCTATAGGGAAAACAGCTTTAGCTATAGACATGGCGATAAATCTTGCGGTTACTCAACAGCGTAGAGTTGGTTTCCTATCTCTAGAAATGAGCGCAGGTCAAATTGTTGAGCGGATTATTGCTAATTTAACAGGAATATCTGGTGAAAAATTACAAAGAGGGGATCTCTCTAAAGAAGAATTATTCCGAGTAGAAGAAGCTGGAGAAACAGTTAGAGAATCACATTTTTATATCTGCAGTGATAGTCAGTATAAGCTTAATTTAATCGCGAATCAGATCCAGTTGCTGAGAAAAGAAGATCGAGTAGACGTAATATTTATCGATTACTTGCAGTTGATCAACTCATCGGTTGGAGAAAATCGTCAAAATGAAATAGCAGATATATCTAGAACCTTAAGAGGTTTAGCCTCAGAGCTAAACATTCCTATAGTTTGTTTATCCCAACTATCTAGAAAAGTTGAGGATAGAGCAAATAAAGTTCCCATGCTTTCAGATTTGCGAGACAGCGGTCAAATAGAGCAAGACGCAGATGTGATTTTGTTTATCAATAGGAAGGAATCGTCTTCTAATTGTGAGATAACTGTTGGGAAAAATAGACATGGATCGGTTTTCTCTTCGGTATTACATTTCGATCCAAAAATTAG'..b'CTATTTGACCGCTGTCTCGCAAATCTGAAAGCATGGGAACTTTATTTGCTCTATCCTCAACTTTTCTAGATAGTTGGGATAAACAAACTATAGGAATGTTTAGCTCTGAGGCTAAACCTCTTAAGGTTCTAGATATATCTGCTATTTCATTTTGACGATTTTCTCCAACCGATGAGTTGATCAACTGCAAGTAATCGATAAATATTACGTCTACTCGATCTTCTTTTCTCAGCAACTGGATCTGATTCGCGATTAAATTAAGCTTATACTGACTATCACTGCAGATATAAAAATGTGATTCTCTAACTGTTTCTCCAGCTTCTTCTACTCGGAATAATTCTTCTTTAGAGAGATCCCCTCTTTGTAATTTTTCACCAGATATTCCTGTTAAATTAGCAATAATCCGCTCAACAATTTGACCTGCGCTCATTTCTAGAGATAGGAAACCAACTCTACGCTGTTGAGTAACCGCAAGATTTATCGCCATGTCTATAGCTAAAGCTGTTTTCCCTATAGATGGCCTAGCTGCTATAATCACGAAATTACCTTTAGCTAAGATAACTCCTTTATCATCAATATCCTTGTATCCTGTTGGGAAGCCATCAAAGAAAGAATTTTGATTCTCAGAGAACGCTGCTCGTCTTTTTTTATACGAGCCAGCACTCCAATTTCTGACTGTGAGAATATATCATAAATAGACCGGCCTCTAGCGCTGCGAATAGAAAAAGTCTTTGCTATAGCACTATCAAGCCTTCCCTTTATACGCTCAAGCAATAGAAACGGAGATCTACGCAATGGATTTTCATTGTACTCATTAAACGAGCGGAAAATGAAATTGCTCAAATTTTCTTCAGCGCTACACACGCTCAAATCATCGAGGAAAACCGTATGAGAAACGGATCTAAGCTTGTCATTTGATAAAGCATCATGCAACATTAACCCGAGATACGATTTGTCCATATCTTTGATACGACGCCGCAAAAGCTCTTCCCAAGCCGAGTCTACAGTTATAGGTAATCCATTGTCTTTTAAGTATTTAAATACTATGAATATGTTTTTATGATGGGAACACTTAAACTCATAATTAGCAAGCTGCCTCAGAATATACTCAGTAGAGTCTTCAAATATCAGAGCTTTACCTAACAACGCATACTCGATATCTTGCATGCGATTTTCTATTTCGGAACGAGTTTTCATGTTTATATAAAAAAATACCGAGCGTGCTATCCTGTTAACAACCTGATTATTTCACTAATCAGGACATTTTGCGGATAGGTTATATCACGAGGGATTTCATGGGTAAAGGGATTTTATCTTTGCAGCAAGAAATGTCGTTAGAATATAGCGAAAAGTCTTATCAGGAAGTTTTAAAAATTCGCCAAGAATCCTATTGGAAACGCATGAAAAGCTTCTCCTTATTCGAAGTTATTATGCATTGGACCGCATCACTCAACAAACATACTTGTAGATCATATCGAGGATCTTTTTTGTCTTTAGAAAAGATTGGTCTATTGTCTTTGGATATGAATCTGCAAGAGTTTTCCCTTTTAAATCATAATCTAATCCTAGATGCGATTAAAAAAGTTTCCTCTGCCAAGACTTCTTGGACCGAAGGTACTAAACAAGTTCGAGCAGCAAGCTATATTTCCTTAACAAGATTCCTAAACAGGATGACTCAAGGAATAGTCGCTATAGCGCAACCTTCTAAACAAGAAAATAGTCGAACATTTTTTAAAACCAGGGAAATAGTAAAAACGGATGCGATGAACAGTTTGCAAACAGCATCCTTCCTAAAAGAGCTAAAAAAAATCAACGCCCGGGATTGGTTGATCGCCCAGACAATGCTCCAAGGAGGTAAACGCTCCTCTGAAGTCTTAAGCTTGGAGATTAGTCAGATTTGTTTCCAACAAGCTACCATTTCTTTCTCCCAGCTTAAGAACCGTCAGACAGAAAAGAGGATTATTATAACTTATCCTCAGAAGTTTATGCACTTTCTACAAGAGTACATCGGTCAACGAAGAGGTTTTGTCTTCGTAACTCGCTCCGGAAAAATGGTGGGGTTAAGGCAAATCGCCCGCACGTTCTCTCAAGCAGGACTACAAGCTGCAATCCCTTTTAAGATAACCCCGCACGTGCTTCGAGCAACCGCTGTGACGGAGTACAAACGCCTAGGGTGCTCAGACTCCGACATAATGAAGGTCACGGGACACGCAACCGCAAAGATGATATTTGCGTACGATAAATCCTCTCGAGAAGACAATGCTTCAAAGAAGATGGCTCTAATATAGCCTAAAGGTGTTTTTTCTGGCAACAGAATATGAATATAATTTTAATTATATCACAATATTGTGGGTGTTTGTACTAGAGGACTTACCTCTTCCCCAGAACAATAAGAACACACACTTTGTCTCGATGAGAGACAGGAAATACGCATGATTTCCTCATCTTTTAATCCTATTTGCTTTAAATGAATCAAAGCGCTTGCACGAAGTACTCTGGGAGTAATTTTTATTTTCATAGCACTATGGAACTCTGCAAGCCTAAAATTATGCGCAACCTGACTTGTTGTTACAGGAATCCCTATTTTAGAAACAAATACTCTCCCATTTCTCCCACAAGTGTATTTTTGCAACTCTTCCATTAAGCTGATAGGAAATGTGATTAGAATTTTGGTTTCTTTATTCTGTCTTTTTTTAATGCGAAAGGAAATCTGATTGGATGCAAAAAATAGATCGTCTGTGCGCAAAGACAAAATTTCGTCTAACTTACGGATCCCTTGTACAATCAATTTACCGATTAAATAGTCTCTATAATTCACTATCCGGAGCGCTTCAAAAAAAACTGTCCATTCCTGCTTAGAAATCGATTCTGTTTTGATTTTGTCTCGGATTTTAAAAAATGTAGTGTTTCCAAAATCTTTCAATGGAATAGCGGGTTTAATATATCCCTTGGTCAATCTATACAAAAACTTTGTGAAAGATATGTAGCATGCCGCTCTAGCCTGTTTAGAGGCCTCTGAAACGACTTTTCCATTAAAAACATCTAGAGACTTGATTTTAAACAAAGATTCGCTGTGGTCAAGAGAAATAGCCTTTATCAAGGTTTCCGATAAATCCAGAATCTCTAAAGAAACAAGAAAGTTAATCCCAGACGCATAATTTTTTCTAGTTAGATGAGATAAAGTAGATAACCAAATTTCCGACGCGTCCCCAAAAGTTAAGAACAATCTACTTTTATGGAAAGCCATCGAGCCCATTTTCTTAACCAAAGCTATTCAAAATCGGAGCTCTAAGATTTTAAGAAATTTTTTAACAAAAGTCCATTATGACCAAGTCTACCACCCTACCACCAAGAGTTGCAAAGTCTACCACCAAGAGTTGCAAAGTCTACCACCAAGAGTTGCAAAGTCTACCACCAAGAGTTGCAAATCTCTCTCGTAAAATCAAATCCCTAAATAAATATATATATAATAAATATATATATGAGCTGACGGAGGATCAGCTCTTTTGCTTAAAAAGTTCAAAAAGCTGTTGTAGAAGATTTTCGTTATAGGAGGACAAAGAAACTCCGGAACATATGATGCGAAGTATCTCTATTAAGAAATCAGATAATTGGCGATTCTTCTCTGAATCAGACTTATCTATCGTTTCTCTAACGTCTTTGTTTCTAGATGAAGGAAGAAATTGATCCAACACCCTTATCGCCGATGAGTTCGACATTCCACATACTTTCCCTATCACATCGACCTTGGTTTTTAAATCGCCTTTTCTAGCGGCCAAAATATATGCGGATTTATAGGGGATCGATTGAAACTCTTTTTGTAGAGTTTGGTTGGGGAGGTTTATAAAAAGCTCGTAATATGCAAGAGCATTGTAAGCAGAAGACTTAGTTCTAAAAACTAACTCTATCCAAGATGAAAAAGTTGTTGAGGAGAAGTGATCCTTACTCAGGATTTTTCTAGCATTATAGATTTTTTCTCCTAAAAGAAGTACGTGTTG\n' 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| diff -r 59bd28f6265d -r cb1e3db43020 trycycler_reconcile_msa.xml --- a/trycycler_reconcile_msa.xml Mon Dec 13 21:16:05 2021 +0000 +++ b/trycycler_reconcile_msa.xml Wed Mar 29 20:24:48 2023 +0000 |
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| @@ -8,7 +8,7 @@ <version_command>trycycler --version</version_command> <command detect_errors="exit_code"><![CDATA[ #import re - #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier)) + #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier)+".fasta") #set $folder = $name.strip(".fasta") #set $fullpath = "/".join(["selected_cluster",$folder]) mkdir -p "${fullpath}/1_contigs" && @@ -26,7 +26,7 @@ --max_trim_seq $circularisation.max_trim_seq --max_trim_seq_percent $circularisation.max_trim_seq_percent --min_identity $final_check.min_identity - --max_indel_size $final_check.max_indel_size + --min_1kbp_identity $final_check.min_1kbp_identity --threads \${GALAXY_SLOTS:-2} && trycycler msa --cluster_dir "$fullpath" --kmer $msa.kmer @@ -52,7 +52,7 @@ </section> <section name="final_check" title="Reconcile final check" expanded="true"> <param argument="--min_identity" type="integer" min="70" max="100" value="98" label="Min global alignment percentage identity" help="If any of the sequences have a pairwise global alignment percent identity of less than this (default = 98), then the contigs will fail the final check." /> - <param argument="--max_indel_size" type="integer" min="0" max="10000" value="1000" label="Max alignment indel size" help="If any of the sequences have a pairwise alignment indel size of more than this (default = 1000), then the contigs will fail the final check." /> + <param argument="--min_1kbp_identity" type="integer" min="0" value="25" label="Minimum allowed pairwise 1kbp window identity" help="If any of the sequences have lower pairwise window identity, it is discarted." /> </section> <section name="msa" title="Multiple sequence alignment (MSA) options" expanded="true"> <param argument="--kmer" type="integer" min="20" max="45" value="32" label="k-mer size" help="The k-mer size used for sequence partitioning (default = 32)" /> @@ -83,7 +83,7 @@ <param name="max_trim_seq" value="47000" /> </section> <section name="final_check"> - <param name="max_indel_size" value="230" /> + <param name="min_1kbp_identity" value="30" /> </section> <section name="msa"> <param name="kmer" value="30" /> @@ -122,7 +122,7 @@ </section> <section name="final_check"> <param name="min_identity" value="95" /> - <param name="max_indel_size" value="230" /> + <param name="min_1kbp_identity" value="25" /> </section> <section name="msa"> <param name="kmer" value="33" /> @@ -150,7 +150,27 @@ <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' /> <output name='aligned_cluster' file='aligned_cluster_05.fasta' /> </test> - + <test> + <!-- Use similar collection elmement file id as input (wihout extension)--> + <param name='input_cluster' value='cluster_01' /> + <param name="reads" value="reads.fastq.gz" /> + <section name="initial_check"> + <param name="max_mash_dist" value="0.3" /> + </section> + <section name="circularisation"> + <param name="max_add_seq_percentage" value="8" /> + <param name="max_trim_seq" value="45300" /> + </section> + <section name="final_check"> + <param name="min_identity" value="97" /> + </section> + <section name="msa"> + <param name="step" value="1100" /> + <param name="lookahead" value="980" /> + </section> + <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' /> + <output name='aligned_cluster' file='aligned_cluster_05.fasta' /> + </test> </tests> <help><![CDATA[ |