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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
author abims-sbr
date Fri, 01 Feb 2019 10:23:16 -0500
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-1:000000000000 0:90b57ab0bd1d
1 <tool name="Pairwise" id="pairwise" version="2.1.1">
2
3 <description>
4 Find homologous couples by blast with RBH
5 </description>
6
7 <macros>
8 <import>macros.xml</import>
9 </macros>
10
11 <requirements>
12 <expand macro="python_required" />
13 <requirement type="package" version="1.65">biopython</requirement>
14 <requirement type="package" version="0.9.22">diamond</requirement>
15 <requirement type="package" version="2.2.22">blast-legacy</requirement>
16 </requirements>
17
18 <command><![CDATA[
19 #set $infiles = ""
20 #for $input in $inputs
21 ln -s '$input' '$input.element_identifier';
22 #set $infiles = $infiles + $input.element_identifier + ","
23 #end for
24 #set $infiles = $infiles[:-1]
25
26 ln -s $__tool_directory__/scripts/S02_04_keep_one_hit_from_blast.py . &&
27 ln -s $__tool_directory__/scripts/S03_run_second_blast.py . &&
28 ln -s $__tool_directory__/scripts/S05_find_rbh.py . &&
29
30 python -W ignore $__tool_directory__/scripts/S01_run_first_blast.py $infiles ${e_value} $method
31 > ${output};
32 ]]></command>
33
34 <inputs>
35 <param name="inputs" type="data" format="fasta" multiple="true" label="Input fasta files" />
36 <param name="method" type="select" label="Alignment tool to use" help="tblastx is slow and sensitive, diamond is a lot quicker and less sensitive">
37 <option value="tblastx">tblastx</option>
38 <option value="diamond">Diamond</option>
39 </param>
40 <param name="e_value" type="float" value="1e-5" label="e_value" help="e-value for blast." />
41 </inputs>
42
43 <outputs>
44 <data format="txt" name="output" label="Pairwise" />
45 <collection name="output_fasta_dna" type="list" label="Pairwise_DNA">
46 <discover_datasets pattern="__name_and_ext__" directory="outputs_RBH_dna" />
47 </collection>
48 </outputs>
49
50 <tests>
51 <test>
52 <param name="inputs" ftype="fasta" value="inputs_tblastx/AcAcaud_trinity.fasta,inputs_tblastx/AmAmphi_trinity.fasta,inputs_tblastx/ApApomp_trinity.fasta,inputs_tblastx/PfPfiji_trinity.fasta" />
53 <param name="e-value" value="1e-5" />
54 <param name="method" value="tblastx" />
55 <output_collection name="output_fasta_dna" type="list">
56 <element name="RBH_AcAcaud_AmAmphi_dna">
57 <assert_contents>
58 <has_text text=">Ac5_1/1_1.000_160"/>
59 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
60 <has_text text=">Am1_1/1_1.000_160"/>
61 <has_text text=">Ac7_1/1_1.000_160"/>
62 <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>
63 <has_text text=">Am3_1/1_1.000_160"/>
64 <has_text text=">Ac6_1/1_1.000_160"/>
65 <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>
66 <has_text text=">Am2_1/1_1.000_160"/>
67 </assert_contents>
68 </element>
69 <element name="RBH_AcAcaud_PfPfiji_dna">
70 <assert_contents>
71 <has_text text=">Ac8_1/1_1.000_160"/>
72 <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>
73 <has_text text=">Pf8_1/1_1.000_160"/>
74 <has_text text=">Ac5_1/1_1.000_160"/>
75 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>
76 <has_text text=">Pf7_1/1_1.000_160"/>
77 </assert_contents>
78 </element>
79 <element name="RBH_ApApomp_PfPfiji_dna">
80 <assert_contents>
81 <has_text text=">Ap2_1/1_1.000_160"/>
82 <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>
83 <has_text text=">Pf5_1/1_1.000_160"/>
84 <has_text text=">Ap1_1/1_1.000_160"/>
85 <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>
86 <has_text text=">Pf4_1/1_1.000_160"/>
87 <has_text text=">Ap4_1/1_1.000_135"/>
88 <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>
89 <has_text text=">Pf10_1/1_1.000_160"/>
90 <has_text text=">Ap3_1/1_1.000_160"/>
91 <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>
92 <has_text text=">Pf6_1/1_1.000_160"/>
93 </assert_contents>
94 </element>
95 <element name="RBH_AmAmphi_PfPfiji_dna">
96 <assert_contents>
97 <has_text text=">Am8_1/1_1.000_160"/>
98 <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>
99 <has_text text=">Pf9_1/1_1.000_160"/>
100 <has_text text=">Am1_1/1_1.000_160"/>
101 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
102 <has_text text=">Pf7_1/1_1.000_160"/>
103 </assert_contents>
104 </element>
105 </output_collection>
106 </test>
107
108 <test>
109 <param name="inputs" ftype="fasta" value="inputs_diamond/AcAcaud_Trinity.fasta,inputs_diamond/AmAmphi_Trinity.fasta,inputs_diamond/ApApomp_Trinity.fasta,inputs_diamond/PfPfiji_Trinity.fasta" />
110 <param name="e-value" value="1e-5" />
111 <param name="method" value="diamond" />
112 <output_collection name="output_fasta_dna" type="list">
113 <element name="RBH_AcAcaud_AmAmphi_dna">
114 <assert_contents>
115 <has_text text=">Ac5_1/1_1.000_160"/>
116 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
117 <has_text text=">Am1_1/1_1.000_160"/>
118 <has_text text=">Ac7_1/1_1.000_160"/>
119 <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>
120 <has_text text=">Am3_1/1_1.000_160"/>
121 <has_text text=">Ac6_1/1_1.000_160"/>
122 <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>
123 <has_text text=">Am2_1/1_1.000_160"/>
124 </assert_contents>
125 </element>
126 <element name="RBH_AcAcaud_ApApomp_dna">
127 <assert_contents>
128 <has_text text=">Ac23_1/1_1.000_366"/>
129 <has_text text="ACTGAGGCTCGAACACAACAAAAAGGTGATGAGCAGTCAGCACTTAATAGAATATTACAGCAAGTAGCCAGTAA"/>
130 <has_text text=">Ap46_1/1_1.000_217"/>
131 <has_text text="CCACAACCAAGTGGCGGGTATAACAGCACCGAGGCTCGAACACAGCAAAAAGGTGATGAGCAGTCAGCTCTTAA"/>
132 </assert_contents>
133 </element>
134 <element name="RBH_AcAcaud_PfPfiji_dna">
135 <assert_contents>
136 <has_text text=">Ac8_1/1_1.000_160"/>
137 <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>
138 <has_text text=">Pf8_1/1_1.000_160"/>
139 <has_text text=">Ac5_1/1_1.000_160"/>
140 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>
141 <has_text text=">Pf7_1/1_1.000_160"/>
142 </assert_contents>
143 </element>
144 <element name="RBH_AmAmphi_PfPfiji_dna">
145 <assert_contents>
146 <has_text text=">Am8_1/1_1.000_160"/>
147 <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>
148 <has_text text=">Pf9_1/1_1.000_160"/>
149 <has_text text=">Am1_1/1_1.000_160"/>
150 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
151 <has_text text=">Pf7_1/1_1.000_160"/>
152 </assert_contents>
153 </element>
154 <element name="RBH_ApApomp_PfPfiji_dna">
155 <assert_contents>
156 <has_text text=">Ap2_1/1_1.000_160"/>
157 <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>
158 <has_text text=">Pf5_1/1_1.000_160"/>
159 <!--
160 <has_text text=">Ap1_1/1_1.000_160"/>
161 <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>
162 <has_text text=">Pf4_1/1_1.000_160"/>
163 <has_text text=">Ap4_1/1_1.000_160"/>
164 <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>
165 <has_text text=">Pf10_1/1_1.000_160"/>
166 <has_text text=">Ap3_1/1_1.000_160"/>
167 <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>
168 <has_text text=">Pf6_1/1_1.000_160"/>
169 -->
170 </assert_contents>
171 </element>
172 </output_collection>
173 </test>
174 </tests>
175
176 <help>
177
178 @HELP_AUTHORS@
179
180 <![CDATA[
181
182 **Description**
183
184 This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species).
185
186 --------
187
188 **Parameters**
189
190 - 'Input files' : a collection of fasta files (one file per species)
191 - 'e_value' : the blast e-value. By default it's 1e-5.
192 - 'Alignment tool' : choose the sequences alignment tool between tblastx and Diamond. tblastx is more sensitive and Diamond is much faster.
193
194 --------
195
196 **Outputs**
197
198 - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.
199
200 - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are in nucleic format. There are one file per couple of species, and homologous pairs are written by sets of 4 lines :
201
202 Exemple for two homologous pairs for the output file for species X/Y :
203
204 | >Gene_A_species_X_homologous_to_Gene_B_species_Y
205 | Nucleic_sequence_from_filter_assemblies
206 | >Gene_B_species_Y_homologous_to_Gene_A_species_X
207 | Nucleic_sequence_from_filter_assemblies
208 | >Gene_C_species_X_homologous_to_Gene_D_species_Y
209 | Nucleic_sequence_from_filter_assemblies
210 | >Gene_D_species_Y_homologous_to_Gene_C_species_X
211 | Nucleic_sequence_from_filter_assemblies
212
213
214 --------
215
216 **The AdaptSearch Pipeline**
217
218 .. image:: adaptsearch_picture_helps.png
219
220 ---------
221
222 Changelog
223 ---------
224
225 **Version 2.1 - 03/07/2018**
226
227 - Add the possibility to use Diamond instead of tblastx
228
229 **Version 2.0 - 18/04/2017**
230
231 - NEW: Replace the zip between tools by Dataset Collection
232
233
234 **Version 1.0 - 13/04/2017**
235
236 - TEST: Add functional test with planemo
237
238 - IMPROVEMENT: Use conda dependencies for blast, samtools and python
239
240 ]]>
241 </help>
242
243 </tool>