Mercurial > repos > abims-sbr > pogs

diff POGs.xml @ 2:be2128ad0030 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 7e96bd705e9f8e81a04b9553aacddc61e4c2b5bf
author abims-sbr
date Fri, 05 May 2017 11:01:05 -0400
parents b2895c835ea8
children b7bd93fc0ac9
line wrap: on
line diff
--- a/POGs.xml	Thu Apr 13 09:47:11 2017 -0400
+++ b/POGs.xml	Fri May 05 11:01:05 2017 -0400
@@ -9,16 +9,15 @@
 	</macros>
 
 	<requirements>
-		<expand macro="python_required" />
-		<!-- <requirement type="package" version="1.3.1">samtools</requirement> -->
+		<expand macro="python_required" />		
 	</requirements>
 	
   	<command>
 	<![CDATA[
-		python $__tool_directory__/scripts/S01_get_locus_ortholog_part1.py ${zip_file}
+		python $__tool_directory__/scripts/S01_get_locus_orthologs_part1_v2.py ${zip_file}
 		> ${output} &&
 
-		python $__tool_directory__/scripts/S02_get_locus_ortholog_part2.py ${zip}
+		python $__tool_directory__/scripts/S02_get_locus_orthologs_part2_v2.py ${zip} ${minseq} ${paralogs}
 		>> ${output};
 	]]>
   	</command>
@@ -26,6 +25,11 @@
  	<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" />
+		<param name="minseq" type="integer" value="3" label="Drop orthogroups with less than n species" />
+		<param name="paralogs" type="select" label="Paralogs filtering" help="Yes : paralogs sequences will be (naively) filtered to keep only one sequence. No : the whole orthogroup will be removed." >
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
+		</param>
 	</inputs>
 
 	<outputs>
@@ -37,8 +41,17 @@
 		<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" />
+			<param name="minseq" value="2" />
+			<param name="paralogs" value="no" />
 			<output name="output" value="test_03.out" />
 		</test>
+		<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" />
+			<param name="minseq" value="2" />
+			<param name="paralogs" value="yes" />
+			<output name="output" value="test_03b.out" />
+		</test>
 	</tests>	
 
 	<help>
@@ -51,6 +64,7 @@
 | 
 | The script was written by **Eric Fontanillas**.
 | The wrapper was written by **Julie Baffard**.
+| Last improvments (paralogous filtering and code factoring) made by Victor Mataigne.
 
 
 --------
@@ -92,112 +106,6 @@
 
 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" />