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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
author abims-sbr
date Thu, 13 Apr 2017 05:46:54 -0400
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children be2128ad0030
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<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 : [['&gt;Ac111_5/5_0.688_714', '&gt;Ap70_3/8_0.688_1127'], ['&gt;Ac99_4/4_0.571_7188', '&gt;Ap74_6/9_0.406_9467'], ['&gt;Ac200_7/8_0.694_1836', '&gt;Ap53_1/1_1.000_938'], 
| ['&gt;Ac181_6/10_0.432_8240', '&gt;Ap103_3/10_0.420_9102'], ['&gt;Ac4_2/2_1.000_230', '&gt;Ap27_4/6_0.556_8404'], ['&gt;Ac189_9/10_0.839_7194', '&gt;Ap97_3/4_0.452_3023'], 
| ['&gt;Ac145_4/5_0.538_1334', '&gt;Ap168_5/6_0.824_2007'], ['&gt;Ac178_1/1_1.000_758', '&gt;Ap202_3/3_0.905_2656'], ['&gt;Ac100_1/2_1.000_2338', '&gt;Ap77_5/8_0.405_866'], 
| ['&gt;Ac86_3/5_0.780_4131', '&gt;Ap41_5/10_0.362_5218'], ['&gt;Ac140_4/4_0.886_637', '&gt;Ap62_1/3_0.667_482'], ['&gt;Ac144_1/1_1.000_4240', '&gt;Ap162_1/1_1.000_4925'], 
| ['&gt;Ac34_3/8_0.548_7600', '&gt;Ap144_6/10_0.690_9671'], ['&gt;Ac187_1/7_0.618_12870', '&gt;Ap73_7/10_0.343_2424'], ['&gt;Ac120_1/1_1.000_522', '&gt;Pf74_1/1_1.000_506'], 
| ['&gt;Ac108_2/10_0.395_1982', '&gt;Pf26_1/1_1.000_1717'], ['&gt;Ac88_4/4_0.833_906', '&gt;Pf102_1/1_1.000_1876'], ['&gt;Ac202_1/1_1.000_247', '&gt;Pf36_2/3_0.800_1482'], 
| ['&gt;Ac121_1/1_1.000_659', '&gt;Pf7_1/1_1.000_2255'], ['&gt;Ac129_1/5_0.636_1798', '&gt;Pf100_2/4_0.625_1698'], ['&gt;Ac172_1/1_1.000_348', '&gt;Pf118_1/1_1.000_1108'], 
| ['&gt;Ac66_3/4_0.462_1465', '&gt;Pf229_1/1_1.000_1541'], ['&gt;Ac47_2/7_0.412_1703', '&gt;Pf1_1/2_1.000_1890'], ['&gt;Ac171_3/3_0.926_338', '&gt;Pf4_1/1_1.000_1337'], 
| ['&gt;Ac194_1/5_0.875_275', '&gt;Pf106_1/2_1.000_994'], ['&gt;Ap2_1/2_1.000_264', '&gt;Pf19_1/1_1.000_1879'], ['&gt;Ap35_1/1_1.000_2505', '&gt;Pf70_1/1_1.000_1462'], 
| ['&gt;Ap116_3/4_0.600_1380', '&gt;Pf78_1/1_1.000_1409'],  ['&gt;Ap193_8/9_0.614_1707', '&gt;Pf21_1/8_0.630_1314'], ['&gt;Ap51_1/2_1.000_4292', '&gt;Pf164_1/1_1.000_1021'], 
| ['&gt;Ap170_1/3_0.778_1303', '&gt;Pf87_2/4_0.700_773'], ['&gt;Ap186_6/10_0.521_4506', '&gt;Pf72_1/1_1.000_2344'],['&gt;Ap114_1/2_1.000_859', '&gt;Pf192_1/1_1.000_957'], 
| ['&gt;Ap65_3/7_0.278_914', '&gt;Pf94_1/1_1.000_1135'], ['&gt;Ap164_4/5_0.560_219', '&gt;Pf163_4/4_0.556_866'], ['&gt;Ap199_3/3_0.846_958', '&gt;Pf58_1/3_0.667_1387'], 
| ['&gt;Ap183_7/8_0.326_2702', '&gt;Pf166_1/2_1.000_2528'], ['&gt;Ap89_3/3_0.905_211', '&gt;Pf3_4/4_0.688_1776'], ['&gt;Ap34_1/1_1.000_2528', '&gt;Pf76_3/3_0.500_1714'], 
| ['&gt;Ap16_1/3_0.714_734', '&gt;Pf139_1/1_1.000_508'], ['&gt;Ap119_9/9_0.595_3402', '&gt;Pf108_1/1_1.000_1932'], ['&gt;Ap120_5/10_0.223_8988', '&gt;Pf57_1/1_1.000_2461'], 
| ['&gt;Ap43_1/3_0.778_644', '&gt;Pf2_1/1_1.000_582']] 
| 
| 3_sp : [['&gt;Ac112_1/2_1.000_2711', '&gt;Ap90_7/10_0.397_2604', '&gt;Pf79_1/1_1.000_4515'], ['&gt;Ac148_1/1_1.000_596', '&gt;Ap32_1/1_1.000_664', '&gt;Pf180_1/2_1.000_2336'], 
| ['&gt;Ac177_1/2_1.000_1664', '&gt;Ap147_1/2_1.000_1728', '&gt;Pf178_1/1_1.000_1671'], ['&gt;Ac124_3/3_0.375_1572', '&gt;Ap177_1/3_0.667_625', '&gt;Pf115_1/1_1.000_557'], 
| ['&gt;Ac53_3/4_0.375_999', '&gt;Ap40_1/1_1.000_1011', '&gt;Pf201_1/1_1.000_908'], ['&gt;Ac65_1/2_0.812_306', '&gt;Ap59_7/10_0.227_2379', '&gt;Pf32_3/3_0.818_1014'], 
| ['&gt;Ac190_7/10_0.319_2573', '&gt;Ap166_7/10_0.279_1859', '&gt;Pf13_7/7_0.514_1779'], ['&gt;Ac1_1/2_1.000_6683', '&gt;Ap55_1/9_1.000_267', '&gt;Pf6_1/2_1.000_3095'], 
| ['&gt;Ac91_2/2_0.696_4298', '&gt;Ap75_5/5_0.810_1434', '&gt;Pf69_1/1_1.000_1712'], ['&gt;Ac29_6/9_0.639_3877', '&gt;Ap124_4/8_0.267_1557', '&gt;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 :
| 
| &gt;Ac111_5/5_0.688_714
| ATCCGGAATGACCTTCGGCGGAGCCAGACACGCTGCTGACATCCGGGCAGACGACATGCACCAGTCGAGTGCCGGAGTGATCAACCTGCAGATGGGCACCAACCAGGGAGCGACCCAAAGCGGCATGTCCATGGGAGGTCGTCGGGACATCAGTT
| AAAAGGGGGCGTTTCACATTTCGTCCAGGATTCTGGAACTGTCCGGATCACAGTGCCACTATCCGTGTTTGATCAATTCAAATCGCTAACTTAAAACGGCCTGTATATAGCTACACTTCATTAACAAAACATTTAGCAATGCCTTATTCTATAACAAGCTACTG
| TATCAGCATAATTATGACTTTCCAATACTTCTTTTTAGCAGATCTTTAATTCTTATTCTTTCTTGTTCGCTGCGTACACTTTTTAACAATAACGTAACATTCTGTATTCATTGATCTATGCAGTTTTATATATTTGGAGTACTTGTTAACTTTAAATATCTGTTGAATGTTA
| CTTTTGAAATGTTGTCTCTAAATATTCGCATTAATTAACGTCGTGTTCTTCATCACAGTCAATGTTAACAGCAGCCATAGCACTTTAATTTATTTTGTTACTTTGTTTATTACGCATGTTTCTAAAATTATTCTTTCATTAAAGCTATTGTTCGTTGCACGTTGATAAGT

ATTGTTGTTGCGTTTCGTGATTCTATACATAATATATTCAAAACAATTAAAAA

| &gt;Ap70_3/8_0.688_1127
| GCAGGCCGGACCAACAAGGGCGCTAGCCAATCCGGAATGACCTTCGGCGGAGCCAGACACGCTGCTGACATCCGGGCAGACGACATGCACCAGTCGAGTGCCGGAGTGATCAACCTACAGATGGGCACCAACCAGGGGGCGTCCCAAAGCGGCA
| TGTCCATGGGAGGCCGTCGGGACATCAGTTAAAAGGGGGCGTTTCACATTTCGTGCCAGCGTTCTGGAACTGTCCGGATCACAGTGCCACCATCCGAGTGTTTGGTCAATTCAAATCGCTAACTTAAAACGGCCTGTATATAGCTACATTTCATTAACAAA
| ACATTTAGCGATGCCTTGTTCTATAACAAATTATTGTATCAGCATAATTATTACTTTCCAGTACTTCTTTATAGCAGATCTTTAATTATTGTTCTTTCTTGTTCGCTGCGTACTTTTTAAAAAGAATACAACATTCTGTATTCATTGATCTATGCAGTTTTATATATTTGGA

GTACTTGTTAACTTTAAATATATGTTAAATGTTACTTTTGAAATGTTGTCTCTAAATATTCGCATTAATTAACGTCGTGCTCTTCATCACAGTCAAAGTTAACATTTAACATATATTTAAAGTTAACAAGTACTCCAAATATATAAAACTGCATAGATCAATGAATACAGA
ATGTTGTATTCTTTTTAAAAAGTACGCAGCGAACAAGAAAGAACAATAATTAAAGATCTGCTATAAAGAAGTACTGGAAAGTAATAATTATGCTGATACAATAATTTGTTATAGAACAAGGCATCGCTAAATGTTTTGTTAATGAAATGTAGCTATATACAGGCCGTTT
TAAGTTAGCGATTTGAATTGACCAAACACTCGGATGGTGGCACTGTGATCCGGACAGTTCCAGAACGCTGGCACGAAATGTGAAACGCCCCCTTTTAACTGATGTCCCGACGGCCTCCCATGGACATGCCGCTTTGGGACGCCCCCTGGTTGGTGCCCA
TCTGTAGGTTGATCACTCCGGCACTCGACTGGTGCATGTCGTCTGCCCGGATGTCAGCAGCGTGTCTGGCTCCGCCGAAGGTCATTCCGGATTGGCTAGCGCCCTTGTTGGATCCAGCTTGCAGACCGATACGGCCTGGCC

| 
| An other example, the file locus_3_sp_5.fasta
| 

&gt;Ac53_3/4_0.375_999
CCGATCTTGTCTGGTGTTTTGCTGCCCCCTAGCGAGTGACGACAAACTCGTTGGTACCTTGCTTAGCGCGATAGAAGGGTTGAACATGTTGGCTGCTGGGCTAAGAACTCTAAAAAGCCTTGCCCCTCGGGGTTGCGTAGCGTGGTCGTGTACTTCGGT
GCATGCCAAGCATACCCTACCAGACTTACCATATGATTACAATGCCCTGGAGCCACACATCAGTGCTGAAATCATGCTGCTGCATCACACCAAGCATCACCAGACGTATGTCAACAACCTGAATGTTGCAGAGGAGAAGTTTCATGAGGCTACAGAGAAA
GGTGATGTAACCACAGCAGTATCACTGATGCCAGCCCTAAGATTTAATGGTGGTGGACACATCAACCATACTATATTTTGGAAGAACATGTCACCAAATGGTGGTGGAGAGCCATCTGGCGAACTGATGGAGGCCATCAAACGTGACTTTGGCTCATTTGAA
AACATGAAGAACATGTTGAGTACATCAACCACTGCAGTGCAAGGCTCTGGCTGGGGATGGCTTGGGTACAATAAAAAGATGAAGAAACTAGAAATTGCCACCTGTGCCAACCAAGATCCATTAGAGGGCACTACAGGTCTCGTCCCGTTGTTTGGCATAG
ATGTCTGGGAACATGCCTATTACTTGCAGTACAAGAATGTTCGTCCAGACTATGTAAAGGCTATTTGGAATGTGGCCAACTGGGATGACATCATGGAACGTTACAACAATGCCAGAAAATAAACTGTTAAACAAATAATTAATATATTAATGTGTTGCAATTTTTG
TCAATTGGTACATACACAATTTTGTTCATAAAGAAAATTGTGATTACTTTCTGGCAACTAGTTCCCAGTGAATACAGCAATTGTTCTGCCAAGGATGCATTTGGATTGAGAAGGCACCCAGAATGGGTTATCCGTGAATGTCTATTGGAATGTGGCACCATACG
ATGTTTACTGTATTAGTTACAATTAAAA

| &gt;Ap40_1/1_1.000_1011
| CTGATGTGTGGCCCCCTAGCGAGTGAAGACAAACTCGATAGCACCCAGACAGTTCTGTTGGTTAGATAAAAGGGAGAAACATGCTGGCTGCTGGGCTAAGAACTCTAAAAAGCCTTGCTCCTCGTGGTGGTCTAGCTTGGTCTTGTACCTCGGTACATGC
| CAAACACACACTGCCAGACTTGCCGTATGATTATAATGCTCTGGAGCCACACATCAGTGCTGAAATCATGTTGCTGCATCACACAAAACATCACCAGACGTATGTGAACAACCTGAATATTGCAGAGGAGAAGTTTCATGAGGCTACCGAGAAAGGCGATG
| TGACCACAGCAGTATCACTGATGCCAGCCCTAAGATTTAATGGTGGTGGACATATCAACCATACTATATTTTGGAAGAACATGTCACCAAATGGTGGTGGAGAACCATCTGGCGAACTGATGGAGGCCATCAAACGTGACTTTGGTTCATTTGAAAACATGA
| AGAACATGCTGAGTACAGCAACCACTGCAGTACAAGGCTCTGGCTGGGGATGGCTTGGGTACAATAAAAAGATGAAGAAACTAGAAATTGCCACCTGTGCCAACCAAGATCCATTAGAGGGCACTACAGGTCTTGTCCCACTGTTTGGTATCGATGTCTG
| GGAACATGCCTATTATTTACAGTACAAGAATGTTCGTCCAGACTATGTAAAGGCTATTTGGAATGTGGCTAACTGGGATGATATCATGGAGCGTTACAACAATGCCAGAAAATAAACTTAAATACATCATTATTTAGTTAATGTGCGACTTTTGTTTGTTAATCAGT
| TCACACACCATTCTATTCACAAAGAAAATGGTGTATTTGCTTTCTGTTCAACTGGTTCCCGGTGAATACAGCAGTTGTTCTGCCAAGGATGTATTTGGATTGAGAAGGCACCAAGAATGGGCTGTCACTGAATGTCAATTGGAATGTAGCCTCAATGTTTACT

GTATTACCTACAATTAAAATGATTATGATATAACCAAG

| &gt;Pf201_1/1_1.000_908
| CTTCTGGAACGATGTTGGCTGGGTATAGAACTTTGGCGAGGGTTATCCCACGTGGTGTCAGCTCCGCTTGGGCAAGTACAATAGTACATAACAAGCACACCTTGCCAGATTTACCATATGATTATAATGCCTTGGAACCACACATCAGTGCTGAAATAATGC

TCCTTCATCATACAAAGCATCACCAGACATATGTGAACAATCTGAATGTAGCTGAAGAAAAGTTTCATGAAGCCACGGAGAAAGGTGATGTCACTACAGCTGTGTCGCTAATGCCAGCACTAAGATTTAATGGCGGAGGACACATCAATCACACCATTTTCT
GGAAGAACATGTCTCCTAATGGCGGAGGAGAGCCTTCTGGCGAGTTGATGGAAGCCATTAAACGTGATTTTGGTTCATTTGAGAATATGAAAAACATGTTAAGTACAGCTACAACAGCTGTCCAAGGATCTGGCTGGGGATGGCTTGGTTATAACAAAAAG
ATGAAAAAGCTCGAGATAGCCACTTGTGCCAACCAGGATCCACTGGAAGGAACAACAGGATTAATTCCACTGTTTGGTATTGACGTCTGGGAGCATGCTTACTATCTGCAATATAAAAATGTACGTCCAGATTATGTTAAAGCTATCTGGAATGTGGCCAACT
GGGATGATATTACAGAGCGCTACAACAATGCGAAGAAATAGATTTGCTGGGACATATGAATAGTGCTTGGCAGAGCCTAATGTTGTGTTTATTTCTGTGTTTCTTATCAATCAGTTGATGTATTAGCCCGGTGTATTGACATGAAGAATTGGACAATGATTTCAAA
TACATTTGAACAATAAATGTATCATGATCAAGCATTATTTTGTTAGTTGTCTCCTCCACTGAGAAGACCAAGTTTAATAAACAACAAACACAGA 
	</help>

	<expand macro="citations" />

</tool>