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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77" |
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added:
pipelign.xml test-data/pipelign-in1.fasta |
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| diff -r 000000000000 -r cd9d1eccda7e pipelign.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pipelign.xml Fri Aug 23 14:47:13 2019 -0400 |
| [ |
| @@ -0,0 +1,87 @@ +<?xml version="1.0"?> +<tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0"> + <description>alignment with pipelign</description> + <macros> + <token name="@VERSION@">0.2</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">pipelign</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + pipelign + --outDir files + --clearExistingDirectory + --inFile '$inFile' + --outFile '$outFile' + --lenThr $lenThr + --alphabet $alphabet + --simPer $simPer + --merge $merge + --thread \${GALAXY_SLOTS:-1} + --mIterateLong $mIterateLong + --mIterateMerge $mIterateMerge + --ambigPer $ambigPer + $keepOrphans $keepBadSeqs $excludeClusters + ]]></command> + <inputs> + <param argument="--inFile" type="data" format="fasta" label="Input sequence file" /> + <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" /> + <param argument="--alphabet" type="select" label="Alphabet for input sequences"> + <option value="dna">DNA</option> + <option value="rna">RNA</option> + <option value="aa">Amino Acids</option> + </param> + <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" /> + <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" /> + <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" /> + <param argument="--merge" type="select" label="Merge strategy"> + <option value="P">Parallel</option> + <option value="C">Consensus</option> + </param> + <param argument="--mIterateLong" type="integer" value="1" min="1" label="Number of iterations to refine long alignments" /> + <param argument="--mIterateMerge" type="integer" value="1" min="1" label="Number of iterations to refine merged alignment" /> + <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" /> + <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" /> + </inputs> + <outputs> + <data name="outFile" format="fasta" /> + </outputs> + <tests> + <test> + <param name="inFile" value="pipelign-in1.fasta" /> + <output name="outFile"> + <assert_contents> + <has_line line=">K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1" /> + <has_line line=">K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1" /> + <has_line line=">K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1" /> + <has_line line=">K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1" /> + <has_line line=">K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1" /> + <has_line line=">K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1" /> + <has_line line=">K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1" /> + <has_line line=">K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +------------------- + +A pipeline for automated multiple sequence alignment, particularly of viral sequences. + +]]> + </help> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{spond, + author = "A.S.Md.M. Hossain, S.D.W.Frost", + title = "Pipelign: an alignment pipeline for viral sequences.", + year = "2019", + note = "https://github.com/asmmhossain/pipelign/", + url = "https://github.com/asmmhossain/pipelign/"} + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r cd9d1eccda7e test-data/pipelign-in1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pipelign-in1.fasta Fri Aug 23 14:47:13 2019 -0400 |
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| b'@@ -0,0 +1,200 @@\n+>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1\n+CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAA\n+>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1\n+GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCAATCAAATCAG\n+>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1\n+ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATTTACCAATACT\n+>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1\n+CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCTTCTGATTTGT\n+>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1\n+CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTA\n+>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1\n+CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATG\n+>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1\n+TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATAATTCCCTTCT\n+>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1\n+AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTCTAGGATCAAC\n+>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1\n+ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT\n+>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1\n+AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTA\n+>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1\n+TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA\n+>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1\n+CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT\n+>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1\n+TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATACTGGAGTATTG\n+>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1\n+CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTGTA\n+>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1\n+TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT\n+>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1\n+CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTATATTTTTTCTT\n+>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1\n+GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGCCATCCAATCA\n+>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1\n+ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCTGAGGATTGGT\n+>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1\n+TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATC\n+>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1\n+AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG\n+>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1\n+GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG\n+>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1\n+GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCACCTCCCAACCC\n+>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1\n+CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGGCGACT\n+>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1\n+GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCC\n+>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1\n+TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTATAAACAATGAG\n+>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1\n+ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTATTACAT\n+>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1\n+TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAATGTCTAACAGC\n+>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1\n+GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAA\n+>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1\n+GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACAT\n+>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1\n+TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAATTAGCCTGTCT\n+>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1\n+GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC\n+>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1\n+TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCTGCTTTTCCTA\n+>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1\n+TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGAAGACGAAGGG\n+>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1\n+GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGAC'..b'|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1\n+GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACATCCCACTAGG\n+>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1\n+TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAACAGCAGTTGTT\n+>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1\n+AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT\n+>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1\n+GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA\n+>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1\n+AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA\n+>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1\n+AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCACTAATAAT\n+>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1\n+CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT\n+>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1\n+GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGT\n+>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1\n+CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACATCATTAGTGT\n+>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1\n+TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTA\n+>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1\n+TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTTGATCTGAGGA\n+>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1\n+ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCTGAGGATTGCT\n+>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1\n+CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGC\n+>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1\n+TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC\n+>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1\n+ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAACTTGTC\n+>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1\n+CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCGACAG\n+>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1\n+TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT\n+>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1\n+TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT\n+>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1\n+CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTCCCCCGCTTAA\n+>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1\n+TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG\n+>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1\n+TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCTATACATTC\n+>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1\n+ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAGTGACCTGAGG\n+>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1\n+GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC\n+>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1\n+TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCATATTGTGAGTC\n+>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1\n+ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTGAAGATCTCGG\n+>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1\n+AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACTATAGCCCTGG\n+>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1\n+GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTGTATTATGACC\n+>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1\n+CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATAATTGCCTTAC\n+>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1\n+AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTCTGTTCCAGAG\n+>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1\n+TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATCTCTAGTTACC\n+>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1\n+GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGA\n+>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1\n+CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT\n+>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1\n+AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTG\n+>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1\n+AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTATTTTGTGCATC\n' 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