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comparison pairwise.xml @ 3:5f68b2fc02c1 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:01:55 -0400
parents e95d4b20c62d
children 6709645eff5d
comparison
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2:a9e072d43516 3:5f68b2fc02c1
1 <?xml version="1.0"?> 1 <tool name="Pairwise" id="pairwise" version="2.0">
2
3 <tool name="Pairwise" id="pairwise" version="1.0">
4 2
5 <description> 3 <description>
6 Run reciproque tblastx pairwise 4 Run reciproque tblastx pairwise
7 </description> 5 </description>
8 6
9 <macros> 7 <macros>
10 <import>macros.xml</import> 8 <import>macros.xml</import>
11 </macros> 9 </macros>
12 10
13 <requirements> 11 <requirements>
14 <expand macro="python_required" /> 12 <expand macro="python_required" />
15 <requirement type="package" version="2.2.22">blast-legacy</requirement> 13 <requirement type="package" version="2.2.22">blast-legacy</requirement>
16 <requirement type="package" version="1.3.1">samtools</requirement> 14 <requirement type="package" version="1.3.1">samtools</requirement>
17 </requirements> 15 </requirements>
18 16
19 <command> 17 <command><![CDATA[
20 <![CDATA[ 18 #set $infiles = ""
21 ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . 19 #for $input in $inputs
22 && 20 ln -s '$input' '$input.element_identifier';
23 ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . 21 #set $infiles = $infiles + $input.element_identifier + ","
24 && 22 #end for
25 ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . 23 #set $infiles = $infiles[:-1]
26 && 24
27 ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . 25 ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . &&
28 && 26 ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . &&
29 ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . 27 ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . &&
30 && 28 ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . &&
31 ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . 29 ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . &&
32 && 30 ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . &&
33 ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . 31 ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . &&
34 && 32 ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . &&
35 ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . 33 ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . &&
36 && 34 ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . &&
37 ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . 35 ln -s $__tool_directory__/scripts/S12_prot2dna.py . &&
38 && 36
39 ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . 37 python $__tool_directory__/scripts/S01_organize_rbh.py $infiles ${e_value} \${GALAXY_SLOTS:-1}
40 &&
41 ln -s $__tool_directory__/scripts/S12_prot2dna.py .
42 &&
43 ln -s $__tool_directory__/scripts/S13_zip.py .
44 &&
45 python $__tool_directory__/scripts/S01_organize_rbh.py 8 ${e_value} ${zip}
46 > ${output}; 38 > ${output};
47 ]]> 39 ]]></command>
48 </command>
49 40
50 <inputs> 41 <inputs>
51 <param name="zip" type="data" format="no_unzip.zip,zip" multiple="true" label="Choose your ZIP file" help="Contains the output of the filter tool" /> 42 <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
52 <param name="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" /> 43 <param name="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" />
53 </inputs> 44 </inputs>
54 45
55 <outputs> 46 <outputs>
56 <data format="txt" name="output" label="Pairwise" /> 47 <data format="txt" name="output" label="Pairwise" />
57 <data format="no_unzip.zip" name="output_zip_DNA" label="Pairwise_zip_DNA" from_work_dir="output_file_DNA.zip" /> 48 <collection name="output_fasta_dna" type="list" label="Pairwise DNA">
58 <data format="no_unzip.zip" name="output_zip_PROT" label="Pairwise_zip_PROT" from_work_dir="output_file_PROT.zip" /> 49 <discover_datasets pattern="__name_and_ext__" directory="outputs_dna" />
50 </collection>
51 <collection name="output_fasta_prot" type="list" label="Pairwise PROT">
52 <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" />
53 </collection>
59 </outputs> 54 </outputs>
60 55
61 <tests> 56 <tests>
62 <test> 57 <test>
63 <param name="zip" ftype="zip" value="test_02_input_pairwise.zip" /> 58 <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" />
64 <param name="e-value" value="1e-5" /> 59 <param name="e-value" value="1e-5" />
65 <output name="output" > 60 <output name="output" >
66 <assert_contents> 61 <assert_contents>
67 <has_line line="('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta')"/> 62 <has_line line="('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta')"/>
68 <has_line line="('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/> 63 <has_line line="('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
69 <has_line line="('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/> 64 <has_line line="('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
70 <has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/> 65 <has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
71 <has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/> 66 <has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
72 <has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/> 67 <has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
73 68
74 <has_text text="Number of pairwises parsed = 2" /> 69 <has_text text="Number of pairwises parsed = 2" />
75 <has_text text="Number of pairwises parsed = 3" /> 70 <has_text text="Number of pairwises parsed = 3" />
76 <has_text text="Number of pairwises parsed = 0" /> 71 <has_text text="Number of pairwises parsed = 0" />
77 <has_text text="Number of pairwises parsed = 5" /> 72 <has_text text="Number of pairwises parsed = 5" />
78 <has_text text="Number of pairwises parsed = 1" /> 73 <has_text text="Number of pairwises parsed = 1" />
79
80 </assert_contents> 74 </assert_contents>
81 </output> 75 </output>
76 <output_collection name="output_fasta_prot" type="list">
77 <element name="ReciprocalBestHits_AmAmphi_AcAcaud" value="outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta" />
78 <element name="ReciprocalBestHits_ApApomp_AcAcaud" value="outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta" />
79 <element name="ReciprocalBestHits_ApApomp_AmAmphi" value="outputs_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta" />
80 <element name="ReciprocalBestHits_PfPfiji_AcAcaud" value="outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta" />
81 <element name="ReciprocalBestHits_PfPfiji_AmAmphi" value="outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta" />
82 <element name="ReciprocalBestHits_PfPfiji_ApApomp" value="outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" />
83 </output_collection>
84 <output_collection name="output_fasta_dna" type="list">
85 <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" />
86 <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud.fasta" />
87 <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi.fasta" />
88 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" />
89 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" />
90 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" />
91 </output_collection>
82 </test> 92 </test>
83 </tests> 93 </tests>
84 94
85 <help> 95 <help>
96
97 @HELP_AUTHORS@
86 98
87 ============ 99 ============
88 What it does 100 What it does
89 ============ 101 ============
90 102
91 | This tool takes a zip archive containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons. 103 | This tool takes a 'data collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons.
92 | There are 3 outputs. 104 | There are 3 outputs.
93 | 105 |
94 | The run blast was written by the **NCBI**.
95 | The script was written by **Eric Fontanillas**.
96 | The wrapper was written by **Julie Baffard**.
97 106
98 -------- 107 --------
99 108
100 ========== 109 ==========
101 Parameters 110 Parameters
102 ========== 111 ==========
103 112
104 The choice of parameters is possible : 113 The choice of parameters is possible :
105 114
106 **-e** : 115 **-e** :
107 | is the option for the choice of the e-value. 116 | is the option for the choice of the e-value.
108 | By default it's 10. 117 | By default it's 10.
109 | 118 |
110 119
111 -------- 120 --------
112 121
113 ======= 122 =======
114 Outputs 123 Outputs
115 ======= 124 =======
116 125
117 This tool, produces the following files : 126 This tool, produces the following files :
118 127
119 **Pairwise** : 128 **Pairwise**:
120 | is the general output. It gives the information about what the tool is doing (for each pairwise). 129 | is the general output. It gives the information about what the tool is doing (for each pairwise).
121 | 130 |
122 131
123 **Pairwise_zip_DNA.zip** : 132 **Pairwise DNA**:
124 | is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows : 133 | is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows:
125 | the name of the query sequence 134 | the name of the query sequence
126 | the part of the sequence in nucleotides 135 | the part of the sequence in nucleotides
127 | the name of the match sequence 136 | the name of the match sequence
128 | the part of the sequence in nucleotides 137 | the part of the sequence in nucleotides
129 | 138 |
130 139
131 **Pairwise_zip_PROT.zip** : 140 **Pairwise PROT**:
132 | is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows : 141 | is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows:
133 | the name of the query sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence) 142 | the name of the query sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
134 | the part of the sequence in protein 143 | the part of the sequence in protein
135 | the name of the match sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence) 144 | the name of the match sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
136 | the part of the sequence in protein 145 | the part of the sequence in protein
137 146
138 .. class:: warningmark
139
140 The two 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.
141
142 -------- 147 --------
143 148
144 =============== 149 ===============
145 Working Example 150 Working Example
146 =============== 151 ===============
149 The input files and options 154 The input files and options
150 --------------------------- 155 ---------------------------
151 156
152 **Input files** 157 **Input files**
153 | 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta 158 | 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta
154 | 159 |
155 **Parameters** 160 **Parameters**
156 | e-value = 1e-20 161 | e-value = 1e-20
157 | 162 |
158 163
159 ---------------- 164 ----------------
160 The output files 165 The output files
161 ---------------- 166 ----------------
162 167
163 **Pairwise** 168 **Pairwise**
164 169
165 | -------------------- Pairwise Pp_Ap -------------------- 170 | -------------------- Pairwise Pp_Ap --------------------
166 | 171 |
167 | database : Pp.fasta 172 | database : Pp.fasta
168 | query file : Ap.fasta 173 | query file : Ap.fasta
169 | 174 |
170 | ***** START run BLAST ***** 175 | ***** START run BLAST *****
171 | ***** END run BLAST ***** 176 | ***** END run BLAST *****
172 | 177 |
173 | 178 |
174 | database : Ap.fasta 179 | database : Ap.fasta
175 | query file : only the sequences of Pp.fasta who matched during the last BLAST 180 | query file : only the sequences of Pp.fasta who matched during the last BLAST
176 | 181 |
177 | ***** START run BLAST ***** 182 | ***** START run BLAST *****
178 | ***** END run BLAST ***** 183 | ***** END run BLAST *****
179 | 184 |
180 | [3/5] Get pairs of sequences ... 185 | [3/5] Get pairs of sequences ...
181 | Get list of fasta name involved in RBH 186 | Get list of fasta name involved in RBH
182 | Number of pairwises parsed = 15 187 | Number of pairwises parsed = 15
183 | Get subset of Alvinella db 188 | Get subset of Alvinella db
184 | Get subset of Paralvinella db 189 | Get subset of Paralvinella db
185 | 190 |
186 | -------------------- Pairwise Pp_Ac -------------------- 191 | -------------------- Pairwise Pp_Ac --------------------
187 | 192 |
188 | database : Pp.fasta 193 | database : Pp.fasta
189 | query file : Ac.fasta 194 | query file : Ac.fasta
190 | 195 |
191 | ***** START run BLAST ***** 196 | ***** START run BLAST *****
192 | ***** END run BLAST ***** 197 | ***** END run BLAST *****
193 | 198 |
194 | 199 |
195 | database : Ac.fasta 200 | database : Ac.fasta
196 | query file : only the sequences of Pp.fasta who matched during the last BLAST 201 | query file : only the sequences of Pp.fasta who matched during the last BLAST
197 | 202 |
198 | ***** START run BLAST ***** 203 | ***** START run BLAST *****
199 | ***** END run BLAST ***** 204 | ***** END run BLAST *****
200 | 205 |
201 | [3/5] Get pairs of sequences ... 206 | [3/5] Get pairs of sequences ...
202 | Get list of fasta name involved in RBH 207 | Get list of fasta name involved in RBH
203 | Number of pairwises parsed = 13 208 | Number of pairwises parsed = 13
204 | Get subset of Alvinella db 209 | Get subset of Alvinella db
205 | Get subset of Paralvinella db 210 | Get subset of Paralvinella db
206 | 211 |
207 | 212 |
208 | -------------------- Pairwise Ap_Ac -------------------- 213 | -------------------- Pairwise Ap_Ac --------------------
209 | 214 |
210 | database : Ap.fasta 215 | database : Ap.fasta
211 | query file : Ac.fasta 216 | query file : Ac.fasta
212 |  217 | 
213 | ***** START run BLAST ***** 218 | ***** START run BLAST *****
214 | ***** END run BLAST ***** 219 | ***** END run BLAST *****
215 | 220 |
216 | 221 |
217 | database : Ac.fasta 222 | database : Ac.fasta
218 | query file : only the sequences of Ap.fasta who matched during the last BLAST 223 | query file : only the sequences of Ap.fasta who matched during the last BLAST
219 | 224 |
220 | ***** START run BLAST ***** 225 | ***** START run BLAST *****
221 | ***** END run BLAST ***** 226 | ***** END run BLAST *****
222 | 227 |
223 | [3/5] Get pairs of sequences ... 228 | [3/5] Get pairs of sequences ...
224 | Get list of fasta name involved in RBH 229 | Get list of fasta name involved in RBH
225 | Number of pairwises parsed = 24 230 | Number of pairwises parsed = 24
226 | Get subset of Alvinella db 231 | Get subset of Alvinella db
227 | Get subset of Paralvinella db 232 | Get subset of Paralvinella db
228 | 233 |
229 | 234 |
230 235
231 **Pairwise_output_file_PROT** 236 **Pairwise_output_file_PROT**
232 237
233 | Save as *Galaxy{number}-[Pairwise_output_file_PROT].zip*
234 | If you unzip the file, a number of file appears (number of pairwise) : 19_ReciprocalBestHits_{name_of_pairwise}.fasta
235 | For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta 238 | For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta
236 | 239 |
237 | &gt;Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0 240 | &gt;Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
238 | FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA 241 | FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA
239 | &gt;Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0 242 | &gt;Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
240 | FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA 243 | FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA
241 | &gt;Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0 244 | &gt;Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
242 | LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP 245 | LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP
243 | &gt;Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0 246 | &gt;Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
244 | LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP 247 | LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP
245 | 248 |
246 | 249 |
247 250
248 **Pairwise_output_file_DNA** 251 **Pairwise_output_file_DNA**
249 252
250 | Save as *Galaxy{number}-[Pairwise_output_file_DNA].zip*
251 | If you unzip the file, a number of file appears (number of pairwise) : 25_DNAalignment_corresponding_to_protein_from_19_RBH_{name_of_pairwise}.fasta
252 | For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta 253 | For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta
253 | 254 |
254 | &gt;Ap123_1/1_1.000_748 255 | &gt;Ap123_1/1_1.000_748
255 | CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA 256 | CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA
256 | ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA 257 | ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA
257 | TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA 258 | TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA
258 | CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG 259 | CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG
259 | TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG 260 | TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG
260 | &gt;Pp_146_1/2_1.000_713 261 | &gt;Pp_146_1/2_1.000_713
261 | CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA 262 | CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA
262 | CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG 263 | CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG
263 | AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG 264 | AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG
264 | TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA 265 | TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA
265 | CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT 266 | CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT
266 | &gt;Ap66_1/1_1.000_400 267 | &gt;Ap66_1/1_1.000_400
267 | TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT 268 | TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT
268 | ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG 269 | ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG
269 | CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT 270 | CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT
270 | &gt;Pp_201_2/2_1.000_691 271 | &gt;Pp_201_2/2_1.000_691
271 | ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA 272 | ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA
272 | GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG 273 | GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG
273 274
275 ---------------------------------------------------
276
277 Changelog
278 ---------
279
280 **Version 2.0 - 18/04/2017**
281
282 - NEW: Replace the zip between tools by Dataset Collection
283
284
285 **Version 1.0 - 13/04/2017**
286
287 - TEST: Add funtional test with planemo
288
289 - IMPROVEMENT: Use conda dependencies for blast, samtools and python
290
274 </help> 291 </help>
275 292
276 <expand macro="citations" /> 293 <expand macro="citations" />
277 294
278 </tool> 295 </tool>