Mercurial > repos > abims-sbr > pairwise

annotate pairwise.xml @ 3:5f68b2fc02c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
1 <tool name="Pairwise" id="pairwise" version="2.0">
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
2
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
3 <description>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
4 Run reciproque tblastx pairwise
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
5 </description>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
6
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
7 <macros>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
8 <import>macros.xml</import>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
9 </macros>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
10
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
11 <requirements>
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
12 <expand macro="python_required" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
13 <requirement type="package" version="2.2.22">blast-legacy</requirement>
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
14 <requirement type="package" version="1.3.1">samtools</requirement>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
15 </requirements>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
16
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
17 <command><![CDATA[
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
18 #set $infiles = ""
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
19 #for $input in $inputs
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
20 ln -s '$input' '$input.element_identifier';
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
21 #set $infiles = $infiles + $input.element_identifier + ","
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
22 #end for
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
23 #set $infiles = $infiles[:-1]
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
24
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
25 ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
26 ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
27 ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
28 ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
29 ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
30 ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
31 ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
32 ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
33 ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
34 ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
35 ln -s $__tool_directory__/scripts/S12_prot2dna.py . &&
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
36
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
37 python $__tool_directory__/scripts/S01_organize_rbh.py $infiles ${e_value} \${GALAXY_SLOTS:-1}
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
38 > ${output};
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
39 ]]></command>
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
40
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
41 <inputs>
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
42 <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
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" />
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
44 </inputs>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
45
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
46 <outputs>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
47 <data format="txt" name="output" label="Pairwise" />
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
48 <collection name="output_fasta_dna" type="list" label="Pairwise DNA">
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
49 <discover_datasets pattern="__name_and_ext__" directory="outputs_dna" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
50 </collection>
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
51 <collection name="output_fasta_prot" type="list" label="Pairwise PROT">
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
52 <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
53 </collection>
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
54 </outputs>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
55
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
56 <tests>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
57 <test>
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
58 <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" />
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
59 <param name="e-value" value="1e-5" />
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
60 <output name="output" >
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
61 <assert_contents>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
62 <has_line line="('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta')"/>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
63 <has_line line="('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
64 <has_line line="('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
65 <has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
66 <has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
67 <has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
68
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
69 <has_text text="Number of pairwises parsed = 2" />
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
70 <has_text text="Number of pairwises parsed = 3" />
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
71 <has_text text="Number of pairwises parsed = 0" />
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
72 <has_text text="Number of pairwises parsed = 5" />
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
73 <has_text text="Number of pairwises parsed = 1" />
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
74 </assert_contents>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
75 </output>
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
76 <output_collection name="output_fasta_prot" type="list">
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
77 <element name="ReciprocalBestHits_AmAmphi_AcAcaud" value="outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
78 <element name="ReciprocalBestHits_ApApomp_AcAcaud" value="outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
79 <element name="ReciprocalBestHits_ApApomp_AmAmphi" value="outputs_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
80 <element name="ReciprocalBestHits_PfPfiji_AcAcaud" value="outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
81 <element name="ReciprocalBestHits_PfPfiji_AmAmphi" value="outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
82 <element name="ReciprocalBestHits_PfPfiji_ApApomp" value="outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
83 </output_collection>
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
84 <output_collection name="output_fasta_dna" type="list">
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
85 <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
86 <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
87 <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
88 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
89 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
90 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" />
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
91 </output_collection>
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
92 </test>
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
93 </tests>
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
94
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
95 <help>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
96
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
97 @HELP_AUTHORS@
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
98
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
99 ============
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
100 What it does
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
101 ============
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
102
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
103 | This tool takes a 'data collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons.
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
104 | There are 3 outputs.
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
105 |
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
106
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
107 --------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
108
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
109 ==========
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
110 Parameters
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
111 ==========
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
112
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
113 The choice of parameters is possible :
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
114
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
115 **-e** :
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
116 | is the option for the choice of the e-value.
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
117 | By default it's 10.
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
118 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
119
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
120 --------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
121
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
122 =======
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
123 Outputs
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
124 =======
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
125
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
126 This tool, produces the following files :
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
127
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
128 **Pairwise**:
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
129 | is the general output. It gives the information about what the tool is doing (for each pairwise).
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
130 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
131
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
132 **Pairwise DNA**:
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
133 | is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows:
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
134 | the name of the query sequence
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
135 | the part of the sequence in nucleotides
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
136 | the name of the match sequence
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
137 | the part of the sequence in nucleotides
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
138 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
139
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
140 **Pairwise PROT**:
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
141 | is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows:
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
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)
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
143 | the part of the sequence in protein
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
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)
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
145 | the part of the sequence in protein
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
146
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
147 --------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
148
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
149 ===============
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
150 Working Example
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
151 ===============
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
152
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
153 ---------------------------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
154 The input files and options
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
155 ---------------------------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
156
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
157 **Input files**
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
158 | 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
159 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
160 **Parameters**
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
161 | e-value = 1e-20
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
162 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
163
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
164 ----------------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
165 The output files
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
166 ----------------
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
167
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
168 **Pairwise**
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
169
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
170 | -------------------- Pairwise Pp_Ap --------------------
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
171 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
172 | database : Pp.fasta
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
173 | query file : Ap.fasta
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
174 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
175 | ***** START run BLAST *****
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
176 | ***** END run BLAST *****
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
177 |
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
178 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
179 | database : Ap.fasta
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
180 | query file : only the sequences of Pp.fasta who matched during the last BLAST
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
181 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
182 | ***** START run BLAST *****
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
183 | ***** END run BLAST *****
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
184 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
185 | [3/5] Get pairs of sequences ...
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
186 | Get list of fasta name involved in RBH
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
187 | Number of pairwises parsed = 15
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
188 | Get subset of Alvinella db
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
189 | Get subset of Paralvinella db
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
190 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
191 | -------------------- Pairwise Pp_Ac --------------------
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
192 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
193 | database : Pp.fasta
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
194 | query file : Ac.fasta
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
195 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
196 | ***** START run BLAST *****
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
197 | ***** END run BLAST *****
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
198 |
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
199 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
200 | database : Ac.fasta
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
201 | query file : only the sequences of Pp.fasta who matched during the last BLAST
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
202 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
203 | ***** START run BLAST *****
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
204 | ***** END run BLAST *****
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
205 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
206 | [3/5] Get pairs of sequences ...
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
207 | Get list of fasta name involved in RBH
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
208 | Number of pairwises parsed = 13
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
209 | Get subset of Alvinella db
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
210 | Get subset of Paralvinella db
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
211 |
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
212 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
213 | -------------------- Pairwise Ap_Ac --------------------
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
214 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
215 | database : Ap.fasta
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
216 | query file : Ac.fasta
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
217 | 
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
218 | ***** START run BLAST *****
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
219 | ***** END run BLAST *****
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
220 |
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
221 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
222 | database : Ac.fasta
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
223 | query file : only the sequences of Ap.fasta who matched during the last BLAST
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
224 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
225 | ***** START run BLAST *****
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
226 | ***** END run BLAST *****
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
227 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
228 | [3/5] Get pairs of sequences ...
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
229 | Get list of fasta name involved in RBH
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
230 | Number of pairwises parsed = 24
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
231 | Get subset of Alvinella db
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
232 | Get subset of Paralvinella db
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
233 |
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
234 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
235
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
236 **Pairwise_output_file_PROT**
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
237
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
238 | For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
239 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
240 | &gt;Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
241 | FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
242 | &gt;Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
243 | FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
244 | &gt;Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
245 | LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
246 | &gt;Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
247 | LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
248 |
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
249 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
250
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
251 **Pairwise_output_file_DNA**
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
252
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
253 | For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
254 |
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
255 | &gt;Ap123_1/1_1.000_748
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
256 | CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
257 | ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
258 | TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
259 | CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
260 | TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
261 | &gt;Pp_146_1/2_1.000_713
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
262 | CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
263 | CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
264 | AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
265 | TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
266 | CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
267 | &gt;Ap66_1/1_1.000_400
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
268 | TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
269 | ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
270 | CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
271 | &gt;Pp_201_2/2_1.000_691
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
272 | ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
273 | GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
274
3
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
275 ---------------------------------------------------
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
276
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
277 Changelog
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
278 ---------
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
279
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
280 **Version 2.0 - 18/04/2017**
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
281
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
282 - NEW: Replace the zip between tools by Dataset Collection
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
283
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
284
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
285 **Version 1.0 - 13/04/2017**
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
286
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
287 - TEST: Add funtional test with planemo
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
288
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
289 - IMPROVEMENT: Use conda dependencies for blast, samtools and python
5f68b2fc02c1 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
290
0
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
291 </help>
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
292
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
293 <expand macro="citations" />
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
294
e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
295 </tool>