Mercurial > repos > abims-sbr > pogs
changeset 0:b2895c835ea8 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
| author | abims-sbr |
|---|---|
| date | Thu, 13 Apr 2017 05:46:54 -0400 |
| parents | |
| children | 0037e4e222b1 |
| files | CHANGELOG.md POGs.xml macros.xml test-data/filter_oase_results_for_pogs.zip test-data/test_03.out test-data/test_03_output_Pairwise_PROT_inputPOGS.zip test-data/test_4_output_POGS_input_BlastAlign.zip |
| diffstat | 7 files changed, 243 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CHANGELOG.md Thu Apr 13 05:46:54 2017 -0400 @@ -0,0 +1,7 @@ +Changelog + +Version 1.0 - 13/04/2017 + + - Add functional test with planemo + - Planemo test with conda dependency for python + - Scripts renamed + symlinks to the directory 'scripts'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/POGs.xml Thu Apr 13 05:46:54 2017 -0400 @@ -0,0 +1,205 @@ +<tool name="POGs" id="POGs" version="1.0"> + + <description> + Find orthologous groups + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + <expand macro="python_required" /> + <!-- <requirement type="package" version="1.3.1">samtools</requirement> --> + </requirements> + + <command> + <![CDATA[ + python $__tool_directory__/scripts/S01_get_locus_ortholog_part1.py ${zip_file} + > ${output} && + + python $__tool_directory__/scripts/S02_get_locus_ortholog_part2.py ${zip} + >> ${output}; + ]]> + </command> + + <inputs> + <param name="zip" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Contains the files filter after the tool oase" /> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file " help="Contains homologous sequences in PROTEIC format, ONLY A ZIP FILE" /> + </inputs> + + <outputs> + <data format="txt" name="output" label="POGs" /> + <data format="no_unzip.zip" name="output_zip" label="POGs_locus_orthologs_unaligned" from_work_dir="POGs_locus_orthologs_unaligned.zip" /> + </outputs> + + <tests> + <test> + <param name="zip" ftype="zip" value="filter_oase_results_for_pogs.zip" /> + <param name="zip_file" ftype="zip" value="test_03_output_Pairwise_PROT_inputPOGS.zip" /> + <output name="output" value="test_03.out" /> + </test> + </tests> + + <help> +============ +What it does +============ + +| This tool takes a zip archive containing nucleic fasta sequence files and a zip archive containing a file per pairwise with the homologous sequences (in proteic format). It searches for orthologous sequences. +| There are 2 outputs. +| +| The script was written by **Eric Fontanillas**. +| The wrapper was written by **Julie Baffard**. + + +-------- + +====== +Inputs +====== + +option **Select a zip file containing the input files** : + +| the input zip file must have the extension .ort.zip +| At the beginning, when you upload your input, you have to change the extension .zip to .ort.zip + + +-------- + +======= +Outputs +======= + +This tool, produces the following files : + +**POGs** : + +| is the general output. It gives different informations : number of locus, each locus, ... +| it gives for example, all the locus containing 2 species : +| 2_sp : [[name_of_sequence,name_of_squence],...,[name_of_sequence, name_of_sequence]] +| it's the same for locus containing 3 species, 4 species, ... +| + +**POGs_locus_orthologs_unaligned** : + +| is the output (in zip format) which contains each locus. +| one file corresponding to one locus. + +the sequences of each locus are in nucleic format. + +.. class:: warningmark + +The zip output has to be downloaded (and extracts the files with a file archiver software), you cannot visualize them with the "eye icon" through the interface. + +-------- + +=============== +Working Example +=============== + +--------------- +The input files +--------------- + + +| 3 files with 200 nucleic sequences each : Ac.fasta Ap.fasta Pf.fasta. +| a zip file with 3 files containing the homologous sequences of each pairwise. +| + +---------------- +The output files +---------------- + +**POGs** + +| Number of locus = 56 +| +| NUMBER OF REMAINING LOCUS AFTER 1RST TREATMENT [INTRA LOCUS] = 55 + +NUMBER OF REMAINING LOCUS AFTER 2ND TREATMENT [INTER LOCUS] = 53 + +| 2_sp : [['>Ac111_5/5_0.688_714', '>Ap70_3/8_0.688_1127'], ['>Ac99_4/4_0.571_7188', '>Ap74_6/9_0.406_9467'], ['>Ac200_7/8_0.694_1836', '>Ap53_1/1_1.000_938'], +| ['>Ac181_6/10_0.432_8240', '>Ap103_3/10_0.420_9102'], ['>Ac4_2/2_1.000_230', '>Ap27_4/6_0.556_8404'], ['>Ac189_9/10_0.839_7194', '>Ap97_3/4_0.452_3023'], +| ['>Ac145_4/5_0.538_1334', '>Ap168_5/6_0.824_2007'], ['>Ac178_1/1_1.000_758', '>Ap202_3/3_0.905_2656'], ['>Ac100_1/2_1.000_2338', '>Ap77_5/8_0.405_866'], +| ['>Ac86_3/5_0.780_4131', '>Ap41_5/10_0.362_5218'], ['>Ac140_4/4_0.886_637', '>Ap62_1/3_0.667_482'], ['>Ac144_1/1_1.000_4240', '>Ap162_1/1_1.000_4925'], +| ['>Ac34_3/8_0.548_7600', '>Ap144_6/10_0.690_9671'], ['>Ac187_1/7_0.618_12870', '>Ap73_7/10_0.343_2424'], ['>Ac120_1/1_1.000_522', '>Pf74_1/1_1.000_506'], +| ['>Ac108_2/10_0.395_1982', '>Pf26_1/1_1.000_1717'], ['>Ac88_4/4_0.833_906', '>Pf102_1/1_1.000_1876'], ['>Ac202_1/1_1.000_247', '>Pf36_2/3_0.800_1482'], +| ['>Ac121_1/1_1.000_659', '>Pf7_1/1_1.000_2255'], ['>Ac129_1/5_0.636_1798', '>Pf100_2/4_0.625_1698'], ['>Ac172_1/1_1.000_348', '>Pf118_1/1_1.000_1108'], +| ['>Ac66_3/4_0.462_1465', '>Pf229_1/1_1.000_1541'], ['>Ac47_2/7_0.412_1703', '>Pf1_1/2_1.000_1890'], ['>Ac171_3/3_0.926_338', '>Pf4_1/1_1.000_1337'], +| ['>Ac194_1/5_0.875_275', '>Pf106_1/2_1.000_994'], ['>Ap2_1/2_1.000_264', '>Pf19_1/1_1.000_1879'], ['>Ap35_1/1_1.000_2505', '>Pf70_1/1_1.000_1462'], +| ['>Ap116_3/4_0.600_1380', '>Pf78_1/1_1.000_1409'], ['>Ap193_8/9_0.614_1707', '>Pf21_1/8_0.630_1314'], ['>Ap51_1/2_1.000_4292', '>Pf164_1/1_1.000_1021'], +| ['>Ap170_1/3_0.778_1303', '>Pf87_2/4_0.700_773'], ['>Ap186_6/10_0.521_4506', '>Pf72_1/1_1.000_2344'],['>Ap114_1/2_1.000_859', '>Pf192_1/1_1.000_957'], +| ['>Ap65_3/7_0.278_914', '>Pf94_1/1_1.000_1135'], ['>Ap164_4/5_0.560_219', '>Pf163_4/4_0.556_866'], ['>Ap199_3/3_0.846_958', '>Pf58_1/3_0.667_1387'], +| ['>Ap183_7/8_0.326_2702', '>Pf166_1/2_1.000_2528'], ['>Ap89_3/3_0.905_211', '>Pf3_4/4_0.688_1776'], ['>Ap34_1/1_1.000_2528', '>Pf76_3/3_0.500_1714'], +| ['>Ap16_1/3_0.714_734', '>Pf139_1/1_1.000_508'], ['>Ap119_9/9_0.595_3402', '>Pf108_1/1_1.000_1932'], ['>Ap120_5/10_0.223_8988', '>Pf57_1/1_1.000_2461'], +| ['>Ap43_1/3_0.778_644', '>Pf2_1/1_1.000_582']] +| +| 3_sp : [['>Ac112_1/2_1.000_2711', '>Ap90_7/10_0.397_2604', '>Pf79_1/1_1.000_4515'], ['>Ac148_1/1_1.000_596', '>Ap32_1/1_1.000_664', '>Pf180_1/2_1.000_2336'], +| ['>Ac177_1/2_1.000_1664', '>Ap147_1/2_1.000_1728', '>Pf178_1/1_1.000_1671'], ['>Ac124_3/3_0.375_1572', '>Ap177_1/3_0.667_625', '>Pf115_1/1_1.000_557'], +| ['>Ac53_3/4_0.375_999', '>Ap40_1/1_1.000_1011', '>Pf201_1/1_1.000_908'], ['>Ac65_1/2_0.812_306', '>Ap59_7/10_0.227_2379', '>Pf32_3/3_0.818_1014'], +| ['>Ac190_7/10_0.319_2573', '>Ap166_7/10_0.279_1859', '>Pf13_7/7_0.514_1779'], ['>Ac1_1/2_1.000_6683', '>Ap55_1/9_1.000_267', '>Pf6_1/2_1.000_3095'], +| ['>Ac91_2/2_0.696_4298', '>Ap75_5/5_0.810_1434', '>Pf69_1/1_1.000_1712'], ['>Ac29_6/9_0.639_3877', '>Ap124_4/8_0.267_1557', '>Pf18_43/95_1.000_2422']] +| +| + +**POGs_locus_orthologs_unaligned** + +| Save as *Galaxy{number}-[POGs_locus_orthologs_unaligned].zip* +| If you unzip the file, a number of files are extracted (depends on the number of locus) : locus{nb}_sp{nb_of_species}.fasta +| For example the file locus1_sp2.fasta : +| +| >Ac111_5/5_0.688_714 +| ATCCGGAATGACCTTCGGCGGAGCCAGACACGCTGCTGACATCCGGGCAGACGACATGCACCAGTCGAGTGCCGGAGTGATCAACCTGCAGATGGGCACCAACCAGGGAGCGACCCAAAGCGGCATGTCCATGGGAGGTCGTCGGGACATCAGTT +| AAAAGGGGGCGTTTCACATTTCGTCCAGGATTCTGGAACTGTCCGGATCACAGTGCCACTATCCGTGTTTGATCAATTCAAATCGCTAACTTAAAACGGCCTGTATATAGCTACACTTCATTAACAAAACATTTAGCAATGCCTTATTCTATAACAAGCTACTG +| TATCAGCATAATTATGACTTTCCAATACTTCTTTTTAGCAGATCTTTAATTCTTATTCTTTCTTGTTCGCTGCGTACACTTTTTAACAATAACGTAACATTCTGTATTCATTGATCTATGCAGTTTTATATATTTGGAGTACTTGTTAACTTTAAATATCTGTTGAATGTTA +| CTTTTGAAATGTTGTCTCTAAATATTCGCATTAATTAACGTCGTGTTCTTCATCACAGTCAATGTTAACAGCAGCCATAGCACTTTAATTTATTTTGTTACTTTGTTTATTACGCATGTTTCTAAAATTATTCTTTCATTAAAGCTATTGTTCGTTGCACGTTGATAAGT + +ATTGTTGTTGCGTTTCGTGATTCTATACATAATATATTCAAAACAATTAAAAA + +| >Ap70_3/8_0.688_1127 +| GCAGGCCGGACCAACAAGGGCGCTAGCCAATCCGGAATGACCTTCGGCGGAGCCAGACACGCTGCTGACATCCGGGCAGACGACATGCACCAGTCGAGTGCCGGAGTGATCAACCTACAGATGGGCACCAACCAGGGGGCGTCCCAAAGCGGCA +| TGTCCATGGGAGGCCGTCGGGACATCAGTTAAAAGGGGGCGTTTCACATTTCGTGCCAGCGTTCTGGAACTGTCCGGATCACAGTGCCACCATCCGAGTGTTTGGTCAATTCAAATCGCTAACTTAAAACGGCCTGTATATAGCTACATTTCATTAACAAA +| ACATTTAGCGATGCCTTGTTCTATAACAAATTATTGTATCAGCATAATTATTACTTTCCAGTACTTCTTTATAGCAGATCTTTAATTATTGTTCTTTCTTGTTCGCTGCGTACTTTTTAAAAAGAATACAACATTCTGTATTCATTGATCTATGCAGTTTTATATATTTGGA + +GTACTTGTTAACTTTAAATATATGTTAAATGTTACTTTTGAAATGTTGTCTCTAAATATTCGCATTAATTAACGTCGTGCTCTTCATCACAGTCAAAGTTAACATTTAACATATATTTAAAGTTAACAAGTACTCCAAATATATAAAACTGCATAGATCAATGAATACAGA +ATGTTGTATTCTTTTTAAAAAGTACGCAGCGAACAAGAAAGAACAATAATTAAAGATCTGCTATAAAGAAGTACTGGAAAGTAATAATTATGCTGATACAATAATTTGTTATAGAACAAGGCATCGCTAAATGTTTTGTTAATGAAATGTAGCTATATACAGGCCGTTT +TAAGTTAGCGATTTGAATTGACCAAACACTCGGATGGTGGCACTGTGATCCGGACAGTTCCAGAACGCTGGCACGAAATGTGAAACGCCCCCTTTTAACTGATGTCCCGACGGCCTCCCATGGACATGCCGCTTTGGGACGCCCCCTGGTTGGTGCCCA +TCTGTAGGTTGATCACTCCGGCACTCGACTGGTGCATGTCGTCTGCCCGGATGTCAGCAGCGTGTCTGGCTCCGCCGAAGGTCATTCCGGATTGGCTAGCGCCCTTGTTGGATCCAGCTTGCAGACCGATACGGCCTGGCC + +| +| An other example, the file locus_3_sp_5.fasta +| + +>Ac53_3/4_0.375_999 +CCGATCTTGTCTGGTGTTTTGCTGCCCCCTAGCGAGTGACGACAAACTCGTTGGTACCTTGCTTAGCGCGATAGAAGGGTTGAACATGTTGGCTGCTGGGCTAAGAACTCTAAAAAGCCTTGCCCCTCGGGGTTGCGTAGCGTGGTCGTGTACTTCGGT +GCATGCCAAGCATACCCTACCAGACTTACCATATGATTACAATGCCCTGGAGCCACACATCAGTGCTGAAATCATGCTGCTGCATCACACCAAGCATCACCAGACGTATGTCAACAACCTGAATGTTGCAGAGGAGAAGTTTCATGAGGCTACAGAGAAA +GGTGATGTAACCACAGCAGTATCACTGATGCCAGCCCTAAGATTTAATGGTGGTGGACACATCAACCATACTATATTTTGGAAGAACATGTCACCAAATGGTGGTGGAGAGCCATCTGGCGAACTGATGGAGGCCATCAAACGTGACTTTGGCTCATTTGAA +AACATGAAGAACATGTTGAGTACATCAACCACTGCAGTGCAAGGCTCTGGCTGGGGATGGCTTGGGTACAATAAAAAGATGAAGAAACTAGAAATTGCCACCTGTGCCAACCAAGATCCATTAGAGGGCACTACAGGTCTCGTCCCGTTGTTTGGCATAG +ATGTCTGGGAACATGCCTATTACTTGCAGTACAAGAATGTTCGTCCAGACTATGTAAAGGCTATTTGGAATGTGGCCAACTGGGATGACATCATGGAACGTTACAACAATGCCAGAAAATAAACTGTTAAACAAATAATTAATATATTAATGTGTTGCAATTTTTG +TCAATTGGTACATACACAATTTTGTTCATAAAGAAAATTGTGATTACTTTCTGGCAACTAGTTCCCAGTGAATACAGCAATTGTTCTGCCAAGGATGCATTTGGATTGAGAAGGCACCCAGAATGGGTTATCCGTGAATGTCTATTGGAATGTGGCACCATACG +ATGTTTACTGTATTAGTTACAATTAAAA + +| >Ap40_1/1_1.000_1011 +| CTGATGTGTGGCCCCCTAGCGAGTGAAGACAAACTCGATAGCACCCAGACAGTTCTGTTGGTTAGATAAAAGGGAGAAACATGCTGGCTGCTGGGCTAAGAACTCTAAAAAGCCTTGCTCCTCGTGGTGGTCTAGCTTGGTCTTGTACCTCGGTACATGC +| CAAACACACACTGCCAGACTTGCCGTATGATTATAATGCTCTGGAGCCACACATCAGTGCTGAAATCATGTTGCTGCATCACACAAAACATCACCAGACGTATGTGAACAACCTGAATATTGCAGAGGAGAAGTTTCATGAGGCTACCGAGAAAGGCGATG +| TGACCACAGCAGTATCACTGATGCCAGCCCTAAGATTTAATGGTGGTGGACATATCAACCATACTATATTTTGGAAGAACATGTCACCAAATGGTGGTGGAGAACCATCTGGCGAACTGATGGAGGCCATCAAACGTGACTTTGGTTCATTTGAAAACATGA +| AGAACATGCTGAGTACAGCAACCACTGCAGTACAAGGCTCTGGCTGGGGATGGCTTGGGTACAATAAAAAGATGAAGAAACTAGAAATTGCCACCTGTGCCAACCAAGATCCATTAGAGGGCACTACAGGTCTTGTCCCACTGTTTGGTATCGATGTCTG +| GGAACATGCCTATTATTTACAGTACAAGAATGTTCGTCCAGACTATGTAAAGGCTATTTGGAATGTGGCTAACTGGGATGATATCATGGAGCGTTACAACAATGCCAGAAAATAAACTTAAATACATCATTATTTAGTTAATGTGCGACTTTTGTTTGTTAATCAGT +| TCACACACCATTCTATTCACAAAGAAAATGGTGTATTTGCTTTCTGTTCAACTGGTTCCCGGTGAATACAGCAGTTGTTCTGCCAAGGATGTATTTGGATTGAGAAGGCACCAAGAATGGGCTGTCACTGAATGTCAATTGGAATGTAGCCTCAATGTTTACT + +GTATTACCTACAATTAAAATGATTATGATATAACCAAG + +| >Pf201_1/1_1.000_908 +| CTTCTGGAACGATGTTGGCTGGGTATAGAACTTTGGCGAGGGTTATCCCACGTGGTGTCAGCTCCGCTTGGGCAAGTACAATAGTACATAACAAGCACACCTTGCCAGATTTACCATATGATTATAATGCCTTGGAACCACACATCAGTGCTGAAATAATGC + +TCCTTCATCATACAAAGCATCACCAGACATATGTGAACAATCTGAATGTAGCTGAAGAAAAGTTTCATGAAGCCACGGAGAAAGGTGATGTCACTACAGCTGTGTCGCTAATGCCAGCACTAAGATTTAATGGCGGAGGACACATCAATCACACCATTTTCT +GGAAGAACATGTCTCCTAATGGCGGAGGAGAGCCTTCTGGCGAGTTGATGGAAGCCATTAAACGTGATTTTGGTTCATTTGAGAATATGAAAAACATGTTAAGTACAGCTACAACAGCTGTCCAAGGATCTGGCTGGGGATGGCTTGGTTATAACAAAAAG +ATGAAAAAGCTCGAGATAGCCACTTGTGCCAACCAGGATCCACTGGAAGGAACAACAGGATTAATTCCACTGTTTGGTATTGACGTCTGGGAGCATGCTTACTATCTGCAATATAAAAATGTACGTCCAGATTATGTTAAAGCTATCTGGAATGTGGCCAACT +GGGATGATATTACAGAGCGCTACAACAATGCGAAGAAATAGATTTGCTGGGACATATGAATAGTGCTTGGCAGAGCCTAATGTTGTGTTTATTTCTGTGTTTCTTATCAATCAGTTGATGTATTAGCCCGGTGTATTGACATGAAGAATTGGACAATGATTTCAAA +TACATTTGAACAATAAATGTATCATGATCAAGCATTATTTTGTTAGTTGTCTCCTCCACTGAGAAGACCAAGTTTAATAAACAACAAACACAGA + </help> + + <expand macro="citations" /> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 13 05:46:54 2017 -0400 @@ -0,0 +1,16 @@ +<macros> + + <xml name="python_required"> + <requirement type="package" version="2.7">python</requirement> + </xml> + + <xml name="citations"> + <citations> + <citation type="bibtex">Credits : ABIMS team, Roscoff Marine Station</citation> + <citation type="bibtex">Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.</citation> + <citation type="bibtex">Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard</citation> + <citation type="bibtex">Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor</citation> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.out Thu Apr 13 05:46:54 2017 -0400 @@ -0,0 +1,15 @@ + +Number of locus = 11 + + +NUMBER OF REMAINING LOCUS AFTER 1RST TREATMENT [INTRA LOCUS] = 11 +NUMBER OF REMAINING LOCUS AFTER 2ND TREATMENT [INTER LOCUS] = 11 + + + +Number of species in the locus : 3 + Number of locus : 1 + +Number of species in the locus : 2 + Number of locus : 10 +