Mercurial > repos > abims-sbr > blastalign
annotate BlastAlign.xml @ 5:0d2da4c020dc draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
author | abims-sbr |
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date | Thu, 18 Jan 2018 08:13:26 -0500 |
parents | 9eb5bb56bf41 |
children | e0bea88bb09f |
rev | line source |
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5
0d2da4c020dc
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
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1 <tool name="BlastAlign" id="blastalign" version="2.1"> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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2 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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3 <description> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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4 Align the nucleic acid sequences using BLASTN |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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5 </description> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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6 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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7 <macros> |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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8 <import>macros.xml</import> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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9 </macros> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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10 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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11 <requirements> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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12 <expand macro="python_required" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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13 <requirement type="package" version="1.4">blastalign</requirement> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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14 </requirements> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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15 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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16 <stdio> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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17 <exit_code range="1:" level="fatal" /> |
aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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18 </stdio> |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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19 |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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20 <command><![CDATA[ |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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21 ln -s '$input' '$input.element_identifier'".fasta" && |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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22 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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23 BlastAlign -i '$input.element_identifier'".fasta" |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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24 -m $advanced_option.m |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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25 #if $advanced_option.r != "" |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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26 -r $advanced_option.r |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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27 #end if |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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28 #if $advanced_option.x != "" |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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29 -x $advanced_option.x |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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30 #end if |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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31 -n $advanced_option.n |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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32 #if $advanced_option.s != 0 |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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33 -s $advanced_option.s |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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34 #end if |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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35 && |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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36 ln -s '$input.element_identifier'".fasta.phy" out.phy && |
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49017ea906b5
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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37 ln -s '$input.element_identifier'".fasta.nxs" out.nxs |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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38 #if $fasta_out.value == True |
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49017ea906b5
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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39 && python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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40 #end if |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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41 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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42 ]]></command> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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43 <inputs> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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44 <param name="input" type="data" format="fasta" label="Choose your file" help="A fasta file with nucleotides sequences" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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45 |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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46 <section name="advanced_option" title="Blast advanced options" expanded="True"> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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47 <param argument="-m" type="integer" value="95" min="0" max="100" label="Proportion of gaps allowed in any one sequence in the final alignement" help="default = 95, i.e. only removing sequences with extremely short matches" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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48 <param argument="-r" type="text" area="True" size="1x20" label="Choose a reference sequence" help="default is to search for best candidate (if entered, the sequence will be extracted, written to a separate file, and blasted against the original input file)"/> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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49 <param argument="-x" type="text" area="True" size="5x25" label="Choose the sequences to be excluded from this analysis" help="name of comma-separated sequences " /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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50 <param argument="-n" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Retain original names in output files" help="option F is to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the program" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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51 <param argument="-s" type="integer" value="0" min="0" label="Number of sequences to be used in initial search for reference sequence" help="default (= 0) is to find the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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52 </section> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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53 |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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54 <param name="fasta_out" type="boolean" checked="true" label="Do you want to convert the output phylip in fasta format ? " /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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55 </inputs> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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56 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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57 <outputs> |
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0d2da4c020dc
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
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58 <!-- visible="true" ? --> |
0d2da4c020dc
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
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59 <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" /> |
0d2da4c020dc
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
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60 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" /> |
0d2da4c020dc
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
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61 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" /> |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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62 <filter>fasta_out == True</filter> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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63 </data> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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64 </outputs> |
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aba551b2b79e
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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65 |
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92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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66 <tests> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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67 <test> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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68 <param name="input" ftype="fasta" value="inputs/locus1_sp2.fasta" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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69 <section name="advanced_option"> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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70 <param name="m" value="95" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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71 <param name="r" value="" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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72 <param name="x" value="" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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73 <param name="n" value="False" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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74 <param name="s" value="0" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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75 </section> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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76 <param name="fasta_out" value="True" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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77 <output name="phy" value="outputs/locus1_sp2.phy" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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parents:
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78 <output name="nxs" value="outputs/locus1_sp2.nxs" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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parents:
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79 <output name="fasta" value="outputs/locus1_sp2.fasta" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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80 </test> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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81 <test> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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82 <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" /> |
92615a423389
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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parents:
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83 <section name="advanced_option"> |
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84 <param name="m" value="95" /> |
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85 <param name="r" value="" /> |
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86 <param name="x" value="" /> |
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87 <param name="n" value="False" /> |
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88 <param name="s" value="0" /> |
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89 </section> |
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90 <param name="fasta_out" value="True" /> |
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91 <output name="phy" value="outputs/locus1_sp3.phy" /> |
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92 <output name="nxs" value="outputs/locus1_sp3.nxs" /> |
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93 <output name="fasta" value="outputs/locus1_sp3.fasta" /> |
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94 </test> |
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95 <test> |
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96 <param name="input" ftype="fasta" value="inputs/locus3_sp2.fasta" /> |
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97 <section name="advanced_option"> |
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98 <param name="m" value="95" /> |
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99 <param name="r" value="" /> |
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100 <param name="x" value="" /> |
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101 <param name="n" value="False" /> |
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102 <param name="s" value="0" /> |
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103 </section> |
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104 <param name="fasta_out" value="False" /> |
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105 <output name="phy" value="outputs/locus3_sp2.phy" /> |
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106 <output name="nxs" value="outputs/locus3_sp2.nxs" /> |
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107 </test> |
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108 </tests> |
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109 |
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110 <help> |
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111 <![CDATA[ |
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112 |
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113 . class:: infomark |
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114 |
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115 **Authors** BlastAlign has been written by Robert Belshaw and Aris Katzourakis. The scripts of this tool have been written by Eric Fontanillas. |
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116 |
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117 .. class:: infomark |
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118 |
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119 **Galaxy integration** Julie Baffard and ABiMS Team. |
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120 |
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121 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. |
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122 |
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123 -------- |
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124 |
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125 **Description** |
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126 |
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127 BlastAlign takes a set of nucleic sequences in a file in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLAST+. This Galaxy implementation works with dataset collections, which allows multiple parallels runs of BlastAlign at once on many files. |
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128 |
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129 -------- |
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130 |
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131 **Parameters** |
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132 |
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133 The choice of several parameters for the blast is possible. |
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134 |
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135 **-m : Proportion of gaps allowed in any one sequence in the final alignement** |
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136 integer (between 0 and 100). |
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137 By default : 95%, i.e. only removes sequences with extremely short matches. |
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138 We find 50 the most useful. |
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139 |
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140 **-r : Name of reference sequence** |
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141 text. |
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142 Default is searching for best candidate. |
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143 If entered, the sequence will be extracted, written to a separate file, and blasted against the original input file. |
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144 |
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145 **-x : Name of sequences to be excluded from the analysis** |
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146 text. |
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147 names must be comma-separated. |
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148 |
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149 **-n** |
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150 If checked : retain original names in output files. |
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151 If not checked : output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool. |
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152 Default : checked. |
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153 |
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154 **-s : Number of sequences to be used in initial search for reference sequence** |
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155 integer (between 0 and total number of sequences). |
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156 Default : 0 |
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157 Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large. |
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158 |
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159 -------- |
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160 |
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161 **Outputs** |
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162 |
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163 - 'Alignment_{input.name}_phylip' : |
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164 the aligned sequences in Phylip format. |
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165 |
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166 - 'Alignment_{input.name}_nexus' : |
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167 the aligned sequences in Nexus format. |
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168 |
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169 - 'Alignment_{input_file}_fasta' : |
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170 the aligned sequences in Fasta format if the option "fasta format" is checked. |
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171 |
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172 --------- |
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173 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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174 Changelog |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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175 --------- |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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176 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
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177 **Version 2.1 - 17/01/2018** |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
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178 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
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179 - Applied some bugfixes and minor improvments |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
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180 |
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181 **Version 2.0 - 21/04/2017** |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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182 |
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183 - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files. |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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184 |
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185 **Version 1.0 - 13/04/2017** |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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186 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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187 - TEST: Add funtional test with planemo |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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188 - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python |
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189 |
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190 ]]> |
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191 |
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192 </help> |
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193 |
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194 <expand macro="citations" /> |
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195 |
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196 </tool> |
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197 |