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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:04:08 -0400
parents 78dd6454f6f0
children 988467f963f0
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0:78dd6454f6f0 1:8de21b6eb110
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 2
3 <tool name="MutCount" id="mutcount" version="1.0"> 3 <tool name="MutCount" id="mutcount" version="2.0">
4 <description> 4 <description>
5 This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests. 5 This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests.
6 </description> 6 </description>
7 7
8 <macros> 8 <macros>
9 <import>macros.xml</import> 9 <import>macros.xml</import>
10 </macros> 10 </macros>
11 11
12 <requirements> 12 <requirements>
13 <expand macro="python_required" /> 13 <expand macro="python_required" />
14 </requirements> 14 </requirements>
15 15
16 <command> 16 <command>
17 <![CDATA[ 17 <![CDATA[
18 #if str($method.method_run) == "concat" : 18 #if str($method.method_run) == "concat" :
19 python $__tool_directory__/scripts/S01a_mutcount_pairs.py $method.num_sampled $method.num_iter $method.list_species 19 python '$__tool_directory__/scripts/S01a_mutcount_pairs.py' $method.num_sampled $method.num_iter $method.list_species
20 && 20 &&
21 python $__tool_directory__/scripts/S02a_codon_counting.py ${method.zip_nuc} 21 python '$__tool_directory__/scripts/S02a_codon_counting.py' ${method.concat_nuc}
22 #end if 22 #end if
23 23
24 #if str($method.method_run) == "separated" : 24 #if str($method.method_run) == "separated" :
25 25 #set $infiles = ""
26 #if str($method.format.format_run)== "nucleic" : 26 #for $input in $method.sep_file
27 python $__tool_directory__/scripts/S01b_study_seq_composition_nuc.py ${method.format.zip_nuc} ${method.format.concat_nuc} 27 ln -s '$input' '$input.element_identifier';
28 && 28 #set $infiles = $infiles + $input.element_identifier + ","
29 zip -r multigenes_nucleic.zip OUT/ 29 #end for
30 #end if 30 #set $infiles = $infiles[:-1]
31 31
32 #if str($method.format.format_run)== "proteic" : 32 #if str($method.format_run)== "nucleic" :
33 cp $__tool_directory__/scripts/amino_acid_properties.csv . 33 python '$__tool_directory__/scripts/S02b_study_seq_composition_nuc.py' '$infiles' ${method.concat_phy}
34 && 34 #end if
35 python $__tool_directory__/scripts/S02b_study_seq_composition_aa.py ${method.format.zip_aa} ${method.format.concat_prot} 35
36 && 36 #if str($method.format_run)== "proteic" :
37 zip -r multigenes_proteic.zip OUT/ 37 cp '$__tool_directory__/scripts/amino_acid_properties.csv' .
38 #end if 38 &&
39 #end if 39 python '$__tool_directory__/scripts/S01b_study_seq_composition_aa.py' '$infiles' ${method.concat_phy}
40 #end if
41 #end if
40 ]]> 42 ]]>
41 </command> 43 </command>
42 44
43 <inputs> 45 <inputs>
44 <conditional name="method"> 46 <conditional name="method">
45 <param name="method_run" type="select" label="Which method do you want to use for this tool? "> 47 <param name="method_run" type="select" label="Which method do you want to use for this tool? ">
46 <option value="concat">Concatenated genes in DNA (concatenation from RAxML run)</option> 48 <option value="concat">Concatenated genes in DNA (concatenation from RAxML run)</option>
47 <option value="separated">Set of separated genes (from ORF_Search output "output zip containing files with CDS without indel")</option> 49 <option value="separated">Set of separated genes (from ORF_Search output "output zip containing files with CDS without indel")</option>
48 </param> 50 </param>
49 51
50 <when value="concat"> 52 <when value="concat">
51 <param name="zip_nuc" type="data" format="fasta" label="Choose your fasta file in nucleic format" help="It must contain the concatenated file in NUCLEIC format from Phylogeny tool" /> 53 <param name="concat_nuc" type="data" format="fasta" label="Choose your fasta file in nucleic format" help="It must contain the concatenated file in NUCLEIC format from Phylogeny tool" />
52 <param name="num_sampled" type="integer" value="100" min="0" label="Number of iterations"/> 54 <param name="num_sampled" type="integer" value="100" min="0" label="Number of iterations"/>
53 <param name="num_iter" type="integer" value="100" min="0" label="Number of sampled codons"/> 55 <param name="num_iter" type="integer" value="100" min="0" label="Number of sampled codons"/>
54 <param name="list_species" type="text" size="100" label="List of species" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" /> 56 <param name="list_species" type="text" size="100" label="List of species" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" />
55 </when> 57 </when>
56 58
57 <when value="separated"> 59 <when value="separated">
58 <conditional name="format"> 60 <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? ">
59 <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? "> 61 <option value="nucleic">Nucleic format</option>
60 <option value="nucleic">Nucleic format</option> 62 <option value="proteic">Proteic format</option>
61 <option value="proteic">Proteic format</option> 63 </param>
62 </param> 64 <param name="sep_file" type="data" format="fasta" multiple="true" label="Choose fasta files" help="Concatenated files from ORF_search tool ; in nucleic or proteic, according to the format chosen above" />
63 65 <param name="concat_phy" type="data" format="fasta" label="Concatenated file from Phylogeny step" help="This file is used to retrieve the species names" />
64 <when value="nucleic"> 66 </when>
65 <param name="zip_nuc" type="data" format="fasta,no_unzip.zip" label="Choose your ZIP file" help="It must contain the concatenated file in NUCLEIC format from ORF_search tool" /> 67 </conditional>
66 <param name="concat_nuc" type="data" format="fasta" label="Concatenated file from Phylogeny step" help="This file is used to retrieve the species names" />
67 </when>
68
69 <when value="proteic">
70 <param name="zip_aa" type="data" format="fasta,no_unzip.zip" label="Choose your ZIP file" help="It must contain the concatenated file in PROTEIC format from ORF_search tool" />
71 <param name="concat_prot" type="data" format="fasta" label="concatenated file from Phylogeny step" help="This file is used to retrieve the species names" />
72 </when>
73 </conditional>
74 </when>
75
76 </conditional>
77 </inputs> 68 </inputs>
78 69
79 <outputs> 70 <outputs>
80 <data format="txt" name="output1" label="concatenated_results.txt" from_work_dir="codoncounting_results.txt" > 71 <!-- output concat -->
81 <filter>(method['method_run']=='concat')</filter> 72 <data format="txt" name="output1" label="concatenated_results.txt" from_work_dir="codoncounting_results.txt" >
82 </data> 73 <filter>(method['method_run']=='concat')</filter>
83 <data format="no_unzip.zip" name="output2" label="multigenes_nucleic.zip" from_work_dir="multigenes_nucleic.zip" > 74 </data>
84 <filter>(method['method_run']=='separated' and method['format']['format_run']== 'nucleic')</filter> 75
85 </data> 76 <!-- outputs separated - nucleic -->
86 <data format="no_unzip.zip" name="output3" label="multigenes_proteic.zip" from_work_dir="multigenes_proteic.zip" > 77 <data format="csv" name="nuc_comp" label="nuc_compositions.csv" from_work_dir="OUT/nuc_compositions.csv" >
87 <filter>(method['method_run']=='separated' and method['format']['format_run']== 'proteic')</filter> 78 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
88 </data> 79 </data>
89 </outputs> 80 <data format="csv" name="percent_gc" label="percent_GC.csv" from_work_dir="OUT/percent_GC.csv" >
90 81 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
91 <tests> 82 </data>
92 <test> 83 <data format="csv" name="percent_pur" label="percent_purine.csv" from_work_dir="OUT/percent_purine.csv" >
93 <conditional name="method" > 84 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
94 <param name="method_run" value="concat" /> 85 </data>
95 <param name="zip_nuc" ftype="fasta" value="test_07_output_phylogeny_concatenation.fasta" /> 86 <data format="csv" name="purine_load" label="Purine_Load_Indice.csv" from_work_dir="OUT/Purine_Load_Indice.csv" >
96 <param name="num_sampled" value="100" /> 87 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
97 <param name="num_iter" value="100" /> 88 </data>
98 <param name="list_species" ftype="text" value="Ac,Pu,Am,Ap,Pf,Pg,Th,Ph,Te" /> 89
99 </conditional> 90 <!-- outputs separated - proteic -->
91 <data format="csv" name="prot_comp" label="prot_compositions_All_AA.csv" from_work_dir="OUT/prot_compositions_All_AA.csv" >
92 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
93 </data>
94 <data format="csv" name="ivywrel" label="IVYWREL.csv" from_work_dir="OUT/IVYWREL.csv" >
95 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
96 </data>
97 <data format="csv" name="erk_dnqtsh" label="ERK_DNQTSH.csv" from_work_dir="OUT/ERK_DNQTSH.csv" >
98 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
99 </data>
100 <data format="csv" name="ek_qh" label="EK_QH.csv" from_work_dir="OUT/EK_QH.csv" >
101 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
102 </data>
103 <data format="csv" name="fymink_garp" label="FYMINK_GARP.csv" from_work_dir="OUT/FYMINK_GARP.csv" >
104 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
105 </data>
106 <data format="csv" name="avlimfyw" label="AVLIMFYW.csv" from_work_dir="OUT/AVLIMFYW.csv" >
107 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
108 </data>
109 <data format="csv" name="stnq" label="STNQ.csv" from_work_dir="OUT/STNQ.csv" >
110 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
111 </data>
112 <data format="csv" name="rhkde" label="RHKDE.csv" from_work_dir="OUT/RHKDE.csv" >
113 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
114 </data>
115 <data format="csv" name="payre_mvgds" label="PAYRE-MVGDS.csv" from_work_dir="OUT/PAYRE-MVGDS.csv" >
116 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
117 </data>
118 <data format="csv" name="res_weigth" label="TotalResidueWeight.csv" from_work_dir="OUT/TotalResidueWeight.csv" >
119 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
120 </data>
121 <data format="csv" name="res_vol" label="TotalResidueVolume.csv" from_work_dir="OUT/TotalResidueVolume.csv" >
122 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
123 </data>
124 <data format="csv" name="spec_vol" label="TotalPartialSpecificVolume.csv" from_work_dir="OUT/TotalPartialSpecificVolume.csv" >
125 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
126 </data>
127 <data format="csv" name="hydrat" label="TotalHydratation.csv" from_work_dir="OUT/TotalHydratation.csv" >
128 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
129 </data>
130
131 </outputs>
132
133 <tests>
134 <test>
135 <conditional name="method" >
136 <param name="method_run" value="concat" />
137 <param name="concat_nuc" ftype="fasta" value="test_07_output_phylogeny_concatenation.fasta" />
138 <param name="num_sampled" value="100" />
139 <param name="num_iter" value="100" />
140 <param name="list_species" ftype="text" value="Ac,Pu,Am,Ap,Pf,Pg,Th,Ph,Te" />
141 </conditional>
100 <output name="output1"> 142 <output name="output1">
101 <assert_contents> 143 <assert_contents>
102 <has_text text="counting of Ac"/> 144 <has_text text="counting of Ac"/>
103 <has_text text="counting of Pu"/> 145 <has_text text="counting of Pu"/>
104 <has_text text="counting of Am"/> 146 <has_text text="counting of Am"/>
107 <has_text text="counting of Pg"/> 149 <has_text text="counting of Pg"/>
108 <has_text text="counting of Th"/> 150 <has_text text="counting of Th"/>
109 <has_text text="counting of Ph"/> 151 <has_text text="counting of Ph"/>
110 </assert_contents> 152 </assert_contents>
111 </output> 153 </output>
112 </test> 154 </test>
113 </tests> 155
114 156 <test>
115 <help> 157 <conditional name="method" >
158 <param name="method_run" value="separated" />
159 <param name="format_run" value="nucleic" />
160 <param name="sep_file" ftype="fasta" value="sep_nuc/locus1_sp6_sp6.fasta,sep_nuc/locus1_sp8_sp8.fasta,sep_nuc/locus2_sp6_sp6.fasta" />
161 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" />
162 </conditional>
163 <output name="nuc_comp" >
164 <assert_contents>
165 <has_line line="locus1_sp8_sp8.fasta,0.29870,0.25541,0.19481,0.25108," />
166 </assert_contents>
167 </output>
168 <output name="percent_gc">
169 <assert_contents>
170 <has_line line="locus2_sp6_sp6.fasta,42.70833," />
171 </assert_contents>
172 </output>
173 <output name="percent_pur" >
174 <assert_contents>
175 <has_line line="locus2_sp6_sp6.fasta,56.77083," />
176 </assert_contents>
177 </output>
178 <output name="purine_load" >
179 <assert_contents>
180 <has_line line="locus2_sp6_sp6.fasta,192,14,12,72.91667,62.50000," />
181 </assert_contents>
182 </output>
183 </test>
184
185 <test>
186 <conditional name="method" >
187 <param name="method_run" value="separated" />
188 <param name="format_run" value="proteic" />
189 <param name="sep_file" ftype="fasta" value="sep_aa/locus1_sp6_sp6.fasta,sep_aa/locus1_sp8_sp8.fasta,sep_aa/locus2_sp6_sp6.fasta" />
190 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" />
191 </conditional>
192 <output name="prot_comp" >
193 <assert_contents>
194 <has_line line="locus2_sp6_sp6.fasta,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.03125,0.07812,0.00000,0.04688,0.01562,0.03125,0.03125,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.07812,0.12500,0.00000,0.09375,0.04688,0.04688,0.09375,0.01562,0.09375,0.00000,0.04688,0.01562,0.03125,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812,0.12500,0.00000,0.12500,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.04688,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812," />
195 </assert_contents>
196 </output>
197 <output name="ivywrel">
198 <assert_contents>
199 <has_line line="locus2_sp6_sp6.fasta,21.00000,0.32812,23.00000,0.35938,23.00000,0.35938,22.00000,0.34375,23.00000,0.35938,22.00000,0.34375," />
200 </assert_contents>
201 </output>
202 <output name="res_vol" >
203 <assert_contents>
204 <has_line line="locus2_sp6_sp6.fasta,6575.00000,6593.00000,6587.00000,6645.00000,6631.00000,6645.00000," />
205 </assert_contents>
206 </output>
207 <output name="hydrat" >
208 <assert_contents>
209 <has_line line="locus2_sp6_sp6.fasta,171.50000,171.50000,170.50000,171.00000,171.50000,171.00000," />
210 </assert_contents>
211 </output>
212 </test>
213 </tests>
214
215 <help>
116 216
117 .. class:: infomark 217 .. class:: infomark
118 218
119 **Authors** Eric Fontanillas and Pierre-Guillaume Brun creates the scripts of this pipeline. 219 **Authors** Eric Fontanillas and Pierre-Guillaume Brun creates the scripts of this pipeline.
120 220
130 ======== 230 ========
131 Mutcount 231 Mutcount
132 ======== 232 ========
133 233
134 ----------- 234 -----------
135 Description (temporary - need to be to re-writed) 235 Description
136 ----------- 236 -----------
137 237
138 238
139 This script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences 239 | This script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences. Counting is then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences
140 counting is then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences
141 240
142 In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting 241 | In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting
143 242
144 the script automatically reads the sequences to compare from a file that must be called pairs.txt and located with the .fasta file 243 | The script automatically reads the sequences to compare from a file that must be called pairs.txt (pre-computed by the tool itself) and located with the .fasta file in the pairs.txt file, sequences (let's assume X, Y, Z, U, V) pairs must be written as 'X Y\nU V\nZ V' in this case, codoncounting will count the occurence of codons, amino acids, and types of amino acids in X, U, Z, and count the mutation bias from Y to X, V to U and V to Z X, Y, Z, U, V must be character strings contained in the sequences names in the .fasta file (and be specific to each of them). In pairs.txt, you must write how should be built the bootstrapped resampling of sequences. This must be formated as:'X Y\nbackground: length iterration plusminus listofspecies\nU V\nZ V', explanation below backgrounds must be excplicitely written in the pairs.txt file (the script still integers default parameters). This implies that the first line of pairs.txt should be a background line by default, once the background has been determined, it will be applied to each subsequent analysis until another background is written e.g. 'background: length1 iterration1 plusminus1 listofspecies1\nU V\nZ V\nbackground: length2 iterration2 plusminus2 listofspecies2\nX Y' the first background is applied to U V and Z V and the 2nd background to X Y
145 in the pairs.txt file, sequences (let's assume X, Y, Z, U, V) pairs must be written as 'X Y\nU V\nZ V' 244
146 in this case, codoncounting will count the occurence of codons, amino acids, and types of amino acids in X, U, Z, and count the mutation bias from Y to X, V to U and V to Z 245
147 you can add comments in the pairs.txt file inbetween lines, beginning with '#'. E.G. 'X Y\n#This is my comment\nU V\nZ V' 246 | The script resamples random pairs of aligned codon to determine what countings can be expected under the hypothesis of an homogenous dataset.
148 X, Y, Z, U, V must be character strings contained in the sequences names in the .fasta file (and be specific to each of them) 247 | Countings are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the countings.
149 in pairs.txt, you must write how should be built the bootstrapped resampling of sequences. This must be formated as:'X Y\nbackground: length iterration plusminus listofspecies\nU V\nZ V', explanation below 248 | Then the script simply checks whether the observed data are within the 5% lowest or 5% highest values of the distribution
150 backgrounds must be excplicitely written in the pairs.txt file (the script still integers default parameters). This implies that the first line of pairs.txt should be a background line 249
151 by default, once the background has been determined, it will be applied to each subsequent analysis until another background is written 250 | - length is the number of pairs of codons in each generated alignments (effect on the robustness on the countings performed on this alignement)
152 e.g. 'background: length1 iterration1 plusminus1 listofspecies1\nU V\nZ V\nbackground: length2 iterration2 plusminus2 listofspecies2\nX Y' the first background is applied to U V and Z V and the 2nd background to X Y 251 | - iterration is the number of alignments that will be generated (effect on the resolution of the gaussian distribution)
153 252 | - plusminus can be either '+' or '-', '+' indicates that the following species only must be resampled, '-' that the following species must be excluded from the resampling
154 253 | - listofspecies is the list of species (names contained in the sequences names from the fasta file) that must be included or excluded from the sampling. You can also write 'all' to include every species (in this case, plusminus parameter is ignored)
155 #the script resamples random pairs of aligned codon to determine what countings can be expected under the hypothesis of an homogenous dataset 254
156 #countings are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the countings 255 | Iteration shouldn't be lower that 1000 to have a relatively smooth gaussian distribution, length shouldn't be lower as 1000 to detect codons with relatively low occurence (&lt;1%). For the list of species, you can try to form subgroups depending on the studied parameter (e.g. comparing a terrestrial species with a background composed of marine species)
157 #then the script simply checks whether the observed data are within the 5% lowest or 5% highest values of the distribution
158 in background: length iterration plusminus listofspecies
159 -&gt; length is the number of pairs of codons in each generated alignments (effect on the robustness on the countings performed on this alignement)
160 -&gt; iterration is the number of alignments that will be generated (effect on the resolution of the gaussian distribution)
161 -&gt; plusminus can be either '+' or '-', '+' indicates that the following species only must be resampled, '-' that the following species must be excluded from the resampling
162 -&gt; listofspecies is the list of species (names contained in the sequences names from the fasta file) that must be included or excluded from the sampling. You can also write 'all' to include every species (in this case, plusminus parameter is ignored)
163 #full example: background 5000 10000 + melanogaster elegans sapiens
164 iterration shouldn't be lower that 1000 to have a relatively smooth gaussian distribution, length shouldn't be lower as 1000 to detect codons with relatively low occurence (&lt;1%)
165 for the list of species, you can try to form subgroups depending on the studied parameter (e.g. comparing a terrestrial species with a background composed of marine species)
166 256
167 257
168 258
169 .. class:: infomark 259 .. class:: infomark
170 260
171 261
172 **Important part of this tool (the inputs format)** 262 **Important part of this tool (the inputs format)**
173 263
174 -------- 264 --------
175 265
176 ============ 266 -----------
177 Input format 267 Input files
178 ============ 268 -----------
179 269
180 The script takes as input the DNA alignment (fasta format): python codoncounting.py file_path.fasta 270 | If you choose the concatenated method, the input file is the concatenated genes fasta file (in nucleic format) from a previous run of the toolConcatPhyl.
181 271
182 example. 272 | If you choose the separated method, there are two input files :
183 273 | - A dataset collection containing output files from the CDS_Search tool, the one without indels. These files must be in nucleic or proteic format according to the format chosen along with the method.
184 </help> 274 | - The concatenated genes fasta file from ConcatPhyl, only used here to retrieve species name.
185 275
186 <expand macro="citations" /> 276 ----------
187 277 Parameters
278 ----------
279
280 | There are parameters only for the "Concatenated" method :
281 | - The number of iterations
282 | - The number of sampled codons
283 | - The list of species, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the toll on subgroup of species, not only on the total number of species present in the previous tools.
284
285 ---------
286 Changelog
287 ---------
288
289 **Version 2.0 - 12/07/2017**
290
291 - NEW: Replaced the zip between tools by Dataset Collection
292 - More functional tests
293
294 **Version 1.0 - 14/04/2017**
295
296 - Added the tools to the suite
297 - Added a functional test with planemo
298 - Planemo test using conda dependencies for python
299 - Scripts renamed + symlinks to the directory 'scripts'
300
301 </help>
302
303 <expand macro="citations" />
304
188 </tool> 305 </tool>