blastalign: BlastAlign.xml annotate

annotate BlastAlign.xml @ 0:aba551b2b79e draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122

author	abims-sbr
date	Thu, 13 Apr 2017 05:47:47 -0400
parents
children	92615a423389

rev	line source
0 aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	1 <?xml version="1.0"?>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	2
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	3 <tool name="BlastAlign" id="blastalign" version="1.0">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	4
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	5 <description>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	6 Align the nucleic acid sequences
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	7 </description>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	8
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	9 <macros>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	10 <import>macros.xml</import>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	11 </macros>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	12
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	13 <requirements>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	14 <expand macro="python_required" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	15 <requirement type="package" version="5.22.0">perl</requirement>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	16 <requirement type="package" >blast-legacy</requirement>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	17 <requirement type="package" version="1.4">blastalign</requirement>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	18 </requirements>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	19
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	20 <stdio>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	21 <exit_code range="1:" level="fatal" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	22 </stdio>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	23
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	24 <command>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	25 <![CDATA[
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	26 ln -s $__tool_directory__/scripts/S02_phylip2fasta.py .
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	27 &&
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	28 #if $files.type == "one" :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	29 BlastAlign -i ${files.one_file} -o out
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	30 #if $files.options.option == "yes" :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	31 #if $files.options.options_m.m == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	32 -m ${files.options.options_m.proportion}
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	33 #else :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	34 -m 95
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	35 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	36 #if $files.options.options_r.r == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	37 -r ${files.options.options_r.reference}
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	38 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	39 #if $files.options.options_x.x == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	40 -x ${files.options.options_x.exclusion}
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	41 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	42 #if $files.options.options_n == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	43 -n T
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	44 #else :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	45 -n F
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	46 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	47 #if $files.options.options_s.s == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	48 -s ${files.options.options_s.initialisation}
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	49 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	50 #elif $files.options.option == "no" :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	51 -m 95 -n F
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	52 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	53 >${outfile};
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	54 #if $fasta_out.value == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	55 python $__tool_directory__/scripts/S02_phylip2fasta.py out.phy out.fasta >>${outfile};
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	56 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	57 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	58
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	59 #if $files.type == "many" :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	60 python $__tool_directory__/scripts/S01_prepare_BlastAlign_runs.py ${files.many_files}
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	61 #if $fasta_out.value == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	62 oui
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	63 #else :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	64 non
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	65 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	66 #if $files.options.option == "yes" :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	67 #if $files.options.options_m.m == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	68 ${files.options.options_m.proportion}
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	69 #else :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	70 95
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	71 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	72 #if $files.options.options_n == True :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	73 T
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	74 #else :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	75 F
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	76 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	77 #elif $files.options.option == "no" :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	78 95 F
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	79 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	80 >${outfile};
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	81 #end if
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	82 ]]>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	83 </command>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	84 <inputs>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	85 <conditional name="files">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	86 <param name="type" type="select" label="How many files do you want to align ? ">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	87 <option value="one">Only one file</option>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	88 <option value="many">Many files in zip format</option>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	89 </param>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	90
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	91 <when value="one">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	92 <param name="one_file" type="data" format="fasta" label="Choose your file" help="Only a fasta file with nucleotides sequences" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	93
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	94 <conditional name="options">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	95 <param name="option" type="select" label="Blast advanced options ">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	96 <option value="no">No</option>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	97 <option value="yes">Yes</option>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	98 </param>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	99 <when value="yes">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	100 <conditional name="options_m">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	101 <param name="m" type="boolean" checked="False" label="Proportion of gaps allowed in any one sequence in the final alignement " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	102 <when value="true">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	103 <param name="proportion" type="integer" value="50" min="0" max="100" label="Maximum proportion " help="By default it's 95%" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	104 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	105 <when value="false" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	106 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	107 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	108
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	109 <conditional name="options_r">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	110 <param name="r" type="boolean" label="Choose the reference sequence " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	111 <when value="true" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	112 <param name="reference" type="text" area="True" size="1x20" label="Name " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	113 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	114 <when value="false" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	115 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	116 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	117
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	118 <conditional name="options_x">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	119 <param name="x" type="boolean" label="Choose the sequences to be excluded from this analysis " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	120 <when value="true">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	121 <param name="exclusion" type="text" area="True" size="5x25" label="name of comma-separated sequences " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	122 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	123 <when value="false" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	124 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	125 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	126
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	127 <param name="options_n" type="boolean" label="retain original names in output files "/>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	128
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	129 <conditional name="options_s">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	130 <param name="s" type="boolean" label="Choose the number of sequences to be used in initial search for reference sequence " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	131 <when value="true">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	132 <param name="initialisation" type="integer" value="10" min="0" label="Number of sequences "/>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	133 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	134 <when value="false" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	135 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	136 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	137 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	138 <when value="no" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	139 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	140 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	141 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	142
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	143 <when value="many">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	144 <param name="many_files" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Only a zip file containing fasta file with nucleotides sequences" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	145
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	146 <conditional name="options">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	147 <param name="option" type="select" label="Blast advanced options ">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	148 <option value="no">No</option>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	149 <option value="yes">Yes</option>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	150 </param>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	151 <when value="yes">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	152 <conditional name="options_m">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	153 <param name="m" type="boolean" label="Proportion of gaps allowed in any one sequence in the final alignement " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	154 <when value="true">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	155 <param name="proportion" type="integer" value="50" min="0" max="100" label="Maximum proportion " help="By default it's 95%" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	156 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	157 <when value="false" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	158 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	159 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	160
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	161 <param name="options_n" type="boolean" label="retain original names in output files "/>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	162 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	163 <when value="no" >
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	164 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	165 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	166 </when>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	167 </conditional>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	168
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	169 <param name="fasta_out" type="boolean" checked="True" label="Do you want to convert the output phylip in fasta format ? " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	170 <param name="files_failed" type="boolean" label="Do you want to have a file containing a list of files failed with BlastAlign ? " />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	171 </inputs>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	172
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	173 <outputs>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	174 <data format="txt" name="outfile" label="Alignment" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	175 <data format="phy" name="phy" from_work_dir="out.phy" label="Alignment_${files.one_file.name}_phylip">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	176 <filter>files['type'] == "one"</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	177 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	178 <data format="nxs" name="nxs" from_work_dir="out.nxs" label="Alignment_${files.one_file.name}_nexus">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	179 <filter>files['type'] == "one"</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	180 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	181 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment_${files.one_file.name}_fasta">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	182 <filter>((files['type'] == "one" and fasta_out == True))</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	183 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	184 <data format="no_unzip.zip" name="phy_zip" from_work_dir="Alignment_locus_phy.zip" label="Alignment_locus_phylip">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	185 <filter>files['type'] == "many"</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	186 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	187 <data format="no_unzip.zip" name="nxs_zip" from_work_dir="Alignment_locus_nxs.zip" label="Alignment_locus_nexus">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	188 <filter>files['type'] == "many"</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	189 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	190 <data format="no_unzip.zip" name="fasta_zip" from_work_dir="Alignment_locus_fasta.zip" label="Alignment_locus_fasta">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	191 <filter>((files['type'] == "many" and fasta_out == True))</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	192 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	193
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	194 <data format="txt" name="out_failed" from_work_dir="list_files_failed.txt" label="Alignment_files_failed">
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	195 <filter>files_failed == True</filter>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	196 </data>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	197 </outputs>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	198
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	199 <tests>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	200 <test>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	201 <param name="type" value="many"/>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	202 <param name="many_files" ftype="zip" value="test_4_output_POGS_input_BlastAlign.zip" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	203 <param name="option" value="no" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	204 <param name="fasta_out" value="True" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	205 <param name="files_failed" value="True" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	206 <output name="outfile" value="test_05.out" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	207 </test>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	208 </tests>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	209
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	210 <help>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	211 ============
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	212 What it does
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	213 ============
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	214
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	215 \| This tool takes nucleic sequences in fasta format or zip file containing fasta files and returns a multiple alignement (in Nexus and Phylip formats) using BLAST+
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	216 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	217 \| The script in perl was written by Robert Belshaw and Aris Katzourakis.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	218 \| The script in python was written by Eric Fontanillas.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	219 \| The wrapper was written by Julie Baffard.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	220
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	221 --------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	222
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	223 ==========
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	224 Parameters
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	225 ==========
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	226
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	227 The choice of several parameters for the blast is possible.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	228
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	229 -m [maximum proportion of gaps allowed in any one sequence in the final alignement]
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	230 \| integer (between 0 and 100)
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	231 \| By default : 95%, i.e. only removes sequences with extremely short matches.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	232 \| We find 50 the most useful.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	233 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	234
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	235 -r [name of reference sequence]
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	236 \| text
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	237 \| Default is searching for best candidate.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	238 \| If entered, the sequence will be extracted, written to a separate file, and blasted against the original input file.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	239 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	240
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	241 -x [name of comma-separated sequences to be excluded from this analysis]
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	242 \| text
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	243 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	244
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	245 -n
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	246 \| If it's checked : retain original names in output files.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	247 \| If isn't checked : to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	248 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	249
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	250 -s [number of sequences to be used in initial search for reference sequence]
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	251 \| integer (between 0 and total number of sequences)
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	252 \| Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	253
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	254 .. class:: infomark
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	255
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	256 m and n are the only parameters which can used for the 2 options (one file and many files).
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	257
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	258 --------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	259
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	260 =======
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	261 Outputs
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	262 =======
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	263
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	264 This tool, produces the following files :
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	265
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	266 Alignment
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	267 \| is the output with important informations.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	268 \| when the alignment failed with BlastAlign, the name of the file is writting down this output.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	269 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	270
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	271 Alignement_file_failed
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	272 \| is the output containing the files failed during the run of BlastAlign.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	273 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	274
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	275 Alignment_{inputfile}_phylip
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	276 \| is the output with the aligned sequences in Phylip format when you choose "one file" option.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	277 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	278
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	279 Alignment_{inputfile}_nexus
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	280 \| is the output with the aligned sequences in Nexus format when you choose "one file" option.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	281 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	282
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	283 Alignment_{input_file}_fasta
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	284 \| is the output with the aligned sequences in Fasta format when you choose "one file" and "fasta forme" options
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	285 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	286
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	287 Alignment_locus_phylip
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	288 \| is the output with the aligned sequences in Phylip format when you choose "many files" option.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	289 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	290
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	291 Alignment_locus_nexus
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	292 \| is the output with the aligned sequences in Nexus format when you choose "many files" option.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	293 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	294
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	295 Alignment_locus_fasta
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	296 \| is the output with the aligned sequences in Fasta forme when you choose "many file" and "fasta forme" options
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	297
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	298 .. class:: warningmark
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	299
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	300 The zip outputs have to be downloaded (and extracts the files with a file archiver software), you cannot visualize them with the "eye icon" through the interface.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	301
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	302 --------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	303
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	304 ===============
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	305 Working Example
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	306 ===============
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	307
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	308 ------------------------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	309 The input file and its options
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	310 ------------------------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	311
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	312 Input file
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	313
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	314 \| >Pf210_1/1_1.000_920
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	315 \| CCGGTGGCCATTTTCTGCACCTCGTGGGTTATTGAGCTGAAAGTGGTTCAGCTCACTGTCTGTTAACAGCCGTGTCGGTCTGAGGGTATCACAGTTAATATAATGAATCAAGAGAAGTTGAAGCAGCTCCAGGCCCAAGTCCGCATCGGAGGAAAGGG
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	316 \| CACAGCAAGAAGAAAGAAGAAGGTGATTCACAGAACAGCAACAACAGATGACAAGAAACTGCAAAGTACACTGAAGAAATTGGCAGTAAATAATATTCCGGGTATAGAAGAGGTTAACATGATAAAGGATGACGGGCAAGTAATACATTTTACCAATCCGA
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	317 \| AGGTGCAGGCTTCTCTTCAGTCAAACACATTTGCCATTAATGGCCAAGCCGAAACGAAACAAATCACTGACTTGCTACCCGGTATATTAAATCAGCTGGGGGCTGAAAGTTTAACAAACTTGAAGAAGCTGGCTAAATCTGTGACTGCTGGAGTTGATTC
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	318 \| TGATAACAAGCAGGATGCAGCAGATATTGATGAAGATGATGATGATGTCCCAGAACTGGTTGAAAACTTTGACGAAGCATCGAAGAATGAGGGGACGTAATTCTTCTCCCACTTTATGCCATGGTAGCATCAATCGTTTTGCTGATGATGGCGTGTTTATAC
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	319 \| CTACCACCCAGTGTAGATTTGTCCAGACCTGGCTTGTTTGACATTGCTTGTTGGATTTTGCAACAATATCATGATTAGACTGCCTGGCTTTGTGGCCTAAATACTGTATTAAAGTGTCTGTAAAAGGGAAGCAATTTTTCTATTAAGAAGTTATCCACTAGCAT
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	320 \| ATTGACAGTTTTGCATGTTTGATTTTGTTCCTCGTGCAGGTCAGAACACTGATTGTACAGTGGCTGATTACAGAAAAATTGTATTCAGAGTTAAATAAACACATTATTATCCAAA
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	321 \| >Pp_17_1/1_1.000_930
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	322 \| CCGGTGGCCATTTTCTGCACCTCGTGGGTATCTTGGGTTCGATTTGTATCAGCTCCCTATGTAAAATTAAACAAACTTATAACATAGATTGCAGCTGACAATACAATGAACCAAGAAAAATTAAAACAACTCCAAGCCCAGGTGCGCATTGGAGGCAAGGG
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	323 \| TACAGCAAGAAGAAAGAAGAAGGTCATTCATAGAACAGCAACAACAGATGATAAAAAACTGCAGAGTACATTAAAAAAACTAGCAGTAAATAATATTCCAGGTATAGAAGAGGTTAATATGATAAAAGATGATGGACAGGTAATACATTTTACCAATCCAAAA
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	324 \| GTACAGGCTTCTCTACAGTCAAACACATTTGCTATTAATGGGCAAGCTGAGACAAAACAAATCACCGAATTGTTGCCTGGTATATTAAATCAGCTGGGAGCAGAAAGTTTAACAAATCTGAAGAAACTGGCTACATCCGTGACTGGTGGAGTTGATTCTGAT
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	325 \| AACAAGCCAGAAACAGCAGAAATTGATGAAGACGATGATGATGTTCCAGATTTGGTTGAAAACTTTGACGAGGCATCCAAGAATGAAGGAACGTAATTTGTCATTGGTAGATCCTCCCATAGCCTGATTCTTGTGGCTGGCGACAGCTTGTTTATATTTTAC
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	326
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	327 CCAGTGTAGATTTGTTCAAGAAGGTGTGCTGGCGTTGTTTGAATTTTGTAATAGTACCATGATTTAAATACCCGGTTAACGGCCTACCTGTTATGTAGAAATTGTAGAGAAAAAATTAAATCAATTTTGTATGAACTATAAGCAGCAGCTAATATATTTGCAGTTT
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	328 TACATGTTTATCTGTTCATCAGCATGGGTCAGAGAATGACCGTACTTTGCTGGTGATAGAATGCTTGTATTCAAAGTTTAATAAATGGTTGTAAGCCATTTAAAAAAAAAAAAAAA
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	329
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	330 Parameters
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	331
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	332 \| option : one file. It's the same for the option "many files" except that the output files are in zip format (inside : 1 file corresponding to one output of BlastAlign)
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	333 \| no option for the run Blast. So, by default it's -m 95 -n F
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	334
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	335 ----------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	336 The output files
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	337 ----------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	338
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	339 BlastAlign
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	340
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	341 ********************** BlastAlign **********************
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	342
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	343 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	344 \| This program takes nucleotide sequences in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLASTN
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	345 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	346 \| Input file locus_2_sp_8.fasta has 2 sequences and is 1894 bytes
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	347 \| (maximum number of sequences that will be used to search for the reference sequence is 770)
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	348 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	349 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	350 \| BlastAlign finished: it has produced a multiple alignment of 2 sequences and length 720 by aligning to sequence Pf2101/11000920 (proportion of gaps in each sequence is less than 0.95)
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	351 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	352
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	353 .. class:: infomark
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	354
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	355 \| if you choose the option "many files"
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	356 \| there will be as template output that number of file in the input zip.
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	357 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	358 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	359
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	360 Alignment_{inputfile}_phylip
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	361
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	362 \| 2 720 S
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	363 \| Pf2101/1100 ccggtggccattttctgcacctcgtgggttattgagctgaaagtggttcagctcactgtctgttaacagccgtgtcggtctgagggtatcacagttaatataatgaatcaagagaagttgaagcagctccaggcccaagtccgcatcggaggaaagggcacagcaagaagaaagaagaaggtgattcacagaacagcaacaacagat
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	364
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	365 gacaagaaactgcaaagtacactgaagaaattggcagtaaataatattccgggtatagaagaggttaacatgataaaggatgacgggcaagtaatacattttaccaatccgaaggtgcaggcttctcttcagtcaaacacatttgccattaatggccaagccgaaacgaaacaaatcactgacttgctacccggtatattaaatcagctgggggctgaaag
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	366 tttaacaaacttgaagaagctggctaaatctgtgactgctggagttgattctgataacaagcaggatgcagcagatattgatgaagatgatgatgatgtcccagaactggttgaaaactttgacgaagcatcgaagaatgaggggacgtaattcttctcccactttatgccatggtagcatcaatcgttttgctgatgatggcgtgtttatacctaccacccagtgtaga
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	367 tttgtccagacctggcttgtttgacattgcttgttggattttgcaacaatatcatgattaga
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	368
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	369 \| Pp171/11000 ccggtggccattttctgcacctcgtgggt-------------------------------------------------------------------aatacaatgaaccaagaaaaattaaaacaactccaagcccaggtgcgcattggaggcaagggtacagcaagaagaaagaagaaggtcattcatagaacagcaacaacagatgataaaaaactgcagag
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	370 \| tacattaaaaaaactagcagtaaataatattccaggtatagaagaggttaatatgataaaagatgatggacaggtaatacattttaccaatccaaaagtacaggcttctctacagtcaaacacatttgctattaatgggcaagctgagacaaaacaaatcaccgaattgttgcctggtatattaaatcagctgggagcagaaagtttaacaaatctgaagaaact
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	371 \| ggctacatccgtgactggtggagttgattctgataacaagccagaaacagcagaaattgatgaagacgatgatgatgttccagatttggttgaaaactttgacgaggcatccaagaatgaaggaacgtaatt-----------------------------------------------------------------acccagtgtagatttgt----------------------------------------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	372 \| -------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	373 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	374
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	375 .. class:: infomark
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	376
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	377 \| If you choose the option "many file"
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	378 \| Save as Galaxy{number}-[Alignment_locus_phy].zip
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	379 \| If you unzip the file, a number of files are extracted (depends on the number of locus) : {name_of_file}.phy
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	380 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	381 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	382
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	383 Alignment_{inputfile}_nexus
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	384
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	385 \| #NEXUS
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	386
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	387 [Aligned to seq Pf2101/1100 by BlastAlign. We have excluded sequences with more than 0.95 gaps]
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	388
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	389 BEGIN DATA;
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	390
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	391 \| dimensions ntax=2 nchar=720;
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	392 \| format gap=- datatype=DNA;
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	393 \| matrix
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	394
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	395 Pf2101/1100 ccggtggccattttctgcacctcgtgggttattgagctgaaagtggttcagctcactgtctgttaacagccgtgtcggtctgagggtatcacagttaatataatgaatcaagagaagttgaagcagctccaggcccaagtccgcatcggaggaaagggcacagcaagaagaaagaagaaggtgattcacagaacagcaacaacagat
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	396 gacaagaaactgcaaagtacactgaagaaattggcagtaaataatattccgggtatagaagaggttaacatgataaaggatgacgggcaagtaatacattttaccaatccgaaggtgcaggcttctcttcagtcaaacacatttgccattaatggccaagccgaaacgaaacaaatcactgacttgctacccggtatattaaatcagctgggggctgaaag
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	397 tttaacaaacttgaagaagctggctaaatctgtgactgctggagttgattctgataacaagcaggatgcagcagatattgatgaagatgatgatgatgtcccagaactggttgaaaactttgacgaagcatcgaagaatgaggggacgtaattcttctcccactttatgccatggtagcatcaatcgttttgctgatgatggcgtgtttatacctaccacccagtgtaga
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	398 tttgtccagacctggcttgtttgacattgcttgttggattttgcaacaatatcatgattaga
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	399
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	400 \| Pp171/11000 ccggtggccattttctgcacctcgtgggt-------------------------------------------------------------------aatacaatgaaccaagaaaaattaaaacaactccaagcccaggtgcgcattggaggcaagggtacagcaagaagaaagaagaaggtcattcatagaacagcaacaacagatgataaaaaactgcagag
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	401 \| tacattaaaaaaactagcagtaaataatattccaggtatagaagaggttaatatgataaaagatgatggacaggtaatacattttaccaatccaaaagtacaggcttctctacagtcaaacacatttgctattaatgggcaagctgagacaaaacaaatcaccgaattgttgcctggtatattaaatcagctgggagcagaaagtttaacaaatctgaagaaac
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	402 \| tggctacatccgtgactggtggagttgattctgataacaagccagaaacagcagaaattgatgaagacgatgatgatgttccagatttggttgaaaactttgacgaggcatccaagaatgaaggaacgtaatt-----------------------------------------------------------------acccagtgtagatttgt--------------------------------------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	403 \| -------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	404 \| ;
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	405 \| end;
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	406 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	407
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	408 .. class:: infomark
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	409
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	410 \| If you choose the option "many file"
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	411 \| Save as Galaxy{number}-[Alignment_locus_nxs].zip
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	412 \| If you unzip the file, a number of files are extracted (depends on the number of locus) : {name_of_file}.nxs
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	413 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	414 \|
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	415
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	416 Alignment_{inputfile}_fasta
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	417
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	418 \| >Pf2101/11000920
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	419
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	420 ccggtggccattttctgcacctcgtgggttattgagctgaaagtggttcagctcactgtctgttaacagccgtgtcggtctgagggtatcacagttaatataatgaatcaagagaagttgaagcagctccaggcccaagtccgcatcggaggaaagggcacagcaagaagaaagaagaaggtgattcacagaacagcaacaacagatgacaagaaactg
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	421 caaagtacactgaagaaattggcagtaaataatattccgggtatagaagaggttaacatgataaaggatgacgggcaagtaatacattttaccaatccgaaggtgcaggcttctcttcagtcaaacacatttgccattaatggccaagccgaaacgaaacaaatcactgacttgctacccggtatattaaatcagctgggggctgaaagtttaacaaacttgaa
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	422 gaagctggctaaatctgtgactgctggagttgattctgataacaagcaggatgcagcagatattgatgaagatgatgatgatgtcccagaactggttgaaaactttgacgaagcatcgaagaatgaggggacgtaattcttctcccactttatgccatggtagcatcaatcgttttgctgatgatggcgtgtttatacctaccacccagtgtagatttgtccagacctggc
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	423 ttgtttgacattgcttgttggattttgcaacaatatcatgattaga
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	424
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	425 \| >Pp171/11000930
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	426
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	427 ccggtggccattttctgcacctcgtgggt-------------------------------------------------------------------aatacaatgaaccaagaaaaattaaaacaactccaagcccaggtgcgcattggaggcaagggtacagcaagaagaaagaagaaggtcattcatagaacagcaacaacagatgataaaaaactgcagagtacattaaaaaa
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	428 actagcagtaaataatattccaggtatagaagaggttaatatgataaaagatgatggacaggtaatacattttaccaatccaaaagtacaggcttctctacagtcaaacacatttgctattaatgggcaagctgagacaaaacaaatcaccgaattgttgcctggtatattaaatcagctgggagcagaaagtttaacaaatctgaagaaactggctacatccg
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	429 tgactggtggagttgattctgataacaagccagaaacagcagaaattgatgaagacgatgatgatgttccagatttggttgaaaactttgacgaggcatccaagaatgaaggaacgtaatt-----------------------------------------------------------------acccagtgtagatttgt---------------------------------------------------------
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	430
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	431 .. class:: infomark
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	432
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	433 \| If you choose the option "many file"
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	434 \| Save as Galaxy{number}-[Alignment_locus_fasta].zip
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	435 \| If you unzip the file, a number of files are extracted (depends on the number of locus) : {name_of_file}.fasta
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	436 </help>
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	437
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	438 <expand macro="citations" />
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	439
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122 abims-sbr parents: diff changeset	440 </tool>

Mercurial > repos > abims-sbr > blastalign

annotate BlastAlign.xml @ 0:aba551b2b79e draft