# HG changeset patch
# User abims-sbr
# Date 1549034862 18000
# Node ID b186cae246bdf2e2cdf1a02f4c4822d6b1e3304c
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
diff -r 000000000000 -r b186cae246bd ConcatPhyl.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConcatPhyl.xml Fri Feb 01 10:27:42 2019 -0500
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+ Concatenation and phylogeny
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+ macros.xml
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+
+
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+ raxml
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+
+ > list_files;
+ #end for
+
+ python $__tool_directory__/scripts/S01_concatenate.py
+
+ $infiles_filter_assemblies
+
+ #if $format.format_run == "nucleic" :
+ nucleic
+ #elif $format.format_run == "proteic" :
+ proteic
+ #end if
+
+ list_files
+
+ > ${output};
+
+ raxmlHPC -n galaxy_run
+ #if $format.format_run == "nucleic" :
+ ##-q 05_partitions_gene_NUC
+ -s "03_Concatenation_nuc.phy"
+ -m $format.base_model
+ #elif $format.format_run == "proteic" :
+ ##-q 06_partitions_gene_AA
+ -s 02_Concatenation_aa.phy
+ -m $format.base_model$format.aa_search_matrix
+ #end if
+
+ -p $random_seed
+
+ #if $number_of_runs !="" and $number_of_runs_bootstop =="":
+ -N $number_of_runs
+ -x $rapid_bootstrap_random_seed
+ #elif ($number_of_runs !="" and $number_of_runs_bootstop !="") or ($number_of_runs =="" and $number_of_runs_bootstop !=""):
+ -N $number_of_runs_bootstop
+ -x $rapid_bootstrap_random_seed
+ #end if
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+ -f $search_algorithm
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+ >> ${output};
+ ]]>
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+ format['format_run'] == "proteic" and out == "fasta"
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+ format['format_run'] == "proteic" and out == "phylip"
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+ format['format_run'] == "proteic" and out == "nexus"
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+ format['format_run'] == "nucleic" and out == "fasta"
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+ format['format_run'] == "nucleic" and out == "phylip"
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+ format['format_run'] == "nucleic" and out == "nexus"
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+ raxml1 == True
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+ raxml3 == True
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+ raxml4 == True
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+@HELP_AUTHORS@
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+ 10.1093/bioinformatics/btu033
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diff -r 000000000000 -r b186cae246bd README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Fri Feb 01 10:27:42 2019 -0500
@@ -0,0 +1,14 @@
+Changelog
+
+**Version 2.0 - 06/07/2017**
+
+ - NEW: Replace the zip between tools by Dataset Collection
+
+
+**Version 1.0 - 13/04/2017**
+
+ - Add funtional test with planemo
+
+ - Planemo test with conda dependencies for raxml and python
+
+ - Scripts renamed + symlinks to the directory 'scripts'
diff -r 000000000000 -r b186cae246bd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Feb 01 10:27:42 2019 -0500
@@ -0,0 +1,32 @@
+
+
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+ python
+
+
+
+.. class:: infomark
+
+**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2.
+
+.. class:: infomark
+
+**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station
+
+ | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+ | Credits : Gildas le Corguillé, Misharl Monsoor
+
+---------------------------------------------------
+
+
+
+
+
+ Credits : ABIMS team, Roscoff Marine Station
+ Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+ Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard
+ Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor
+
+
+
+
diff -r 000000000000 -r b186cae246bd scripts/S01_concatenate.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S01_concatenate.py Fri Feb 01 10:27:42 2019 -0500
@@ -0,0 +1,361 @@
+#!/usr/bin/python
+## Author: Eric Fontanillas
+## Last modification: 17/06/2011
+## Subject: find and remove indels
+
+###############################
+##### DEF 0 : Dico fasta #####
+###############################
+def dico(F2):
+ dicoco = {}
+ with open(F2, "r") as file:
+ for name, query in itertools.izip_longest(*[file]*2):
+ if not name:
+ break
+ if name[0] == ">":
+ fasta_name_query = name[:-1]
+ Sn = string.split(fasta_name_query, "||")
+ fasta_name_query = Sn[0]
+ fasta_seq_query = query[:-1]
+ dicoco[fasta_name_query]=fasta_seq_query
+ return dicoco
+###################################################################################
+
+
+####################
+###### DEF 11 ######
+####################
+## Concatenate sequences
+###########################
+def concatenate(L_IN, SPECIES_ID_LIST):
+ ## 4 ## Process files
+ ## 4.1 ## Create the bash and the fasta names entries (name of the species)
+ bash_concat = {}
+
+ for species_ID in SPECIES_ID_LIST:
+ bash_concat[species_ID] = ''
+
+ ln_concat = 0
+ nb_locus = 0
+ pos=1
+ list_genes_position=[]
+ ## 4.2 ## Concatenate
+ for file in L_IN:
+ nb_locus=nb_locus+1
+
+ ## a ## Open alignments
+ dico_seq = dico(file) ### DEF 0 ###
+ ## b ## Get alignment length + genes positions for RAxML
+ key0 = dico_seq.keys()[0]
+ ln = len(dico_seq[key0])
+ ln_concat = ln_concat + ln
+
+ pos_start = pos
+ pos_end = pos+ln-1
+ pos=pos_end+1
+ position="%d-%d" %(pos_start, pos_end)
+ RAxML_name = file[:-6]
+ sublist = [RAxML_name, position]
+ list_genes_position.append(sublist)
+
+ ## c ## Generate "empty" sequence with alignment length * "-"
+ empty_seq = "-" * ln
+
+ ## d ## Concatenate
+ ## d.1 ## Detect missing species in this alignment
+ list_ID=[]
+ list_absent_ID=[]
+ bash_fastaName={}
+ for fasta_name in dico_seq:
+ ID = fasta_name[1:3]
+ list_ID.append(ID)
+ seq = dico_seq[fasta_name]
+ bash_fastaName[ID]=fasta_name
+ for sp_ID in SPECIES_ID_LIST:
+ if sp_ID not in list_ID:
+ list_absent_ID.append(sp_ID)
+
+ for ID in SPECIES_ID_LIST:
+ if ID in list_absent_ID:
+ bash_concat[ID] = bash_concat[ID] + empty_seq
+ else:
+ fasta_name = bash_fastaName[ID]
+ seq = dico_seq[fasta_name]
+ bash_concat[ID] = bash_concat[ID] + seq
+
+ return(bash_concat, ln_concat, nb_locus, list_genes_position)
+####################################
+
+
+########################################
+##### DEF 12 : get codon position #####
+########################################
+def get_codon_position(seq_inORF):
+
+ ln = len(seq_inORF)
+
+ i=0
+ seq_pos1=""
+ seq_pos2=""
+ seq_pos12=""
+ seq_pos3=""
+ while i