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annotate lastsplit.xml @ 10:a07c62dc88f9 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
author iuc
date Sat, 27 Nov 2021 10:11:58 +0000
parents 18ff8319181f
children
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10
a07c62dc88f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
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1 <tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy0" profile="20.01">
0
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2
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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3 <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description>
9
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4 <expand macro="bio_tools"/>
0
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5 <macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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6 <import>macros_last.xml</import>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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7 </macros>
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8
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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9 <requirements>
10
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10 <requirement type="package" version="@TOOL_VERSION@">last</requirement>
0
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11 </requirements>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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12
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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13 <command detect_errors="exit_code"><![CDATA[
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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14 #if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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16 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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17
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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18 last-split
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19
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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20 -f $output_format
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21 #if $db_opts.db_opts_input == 'db'
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22 -g '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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23 #else if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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24 -g 'db_files/lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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25 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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26
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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27 -d $lastsplit_opt.d
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28 -c $lastsplit_opt.c
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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29 -t $lastsplit_opt.t
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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30 -M $lastsplit_opt.M
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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31 -S $lastsplit_opt.S
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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32 -m $lastsplit_opt.m
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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33 $lastsplit_opt.no_split
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34 -b \${GALAXY_MEMORY_MB:-2G}
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35
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36 '$last_align'
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37
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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38 >'$outfile'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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39 ]]></command>
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40
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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41 <inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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42 <expand macro="input_db" />
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43 <param name="last_align" type="data" format="maf" label="LASTal data file" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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44 <param name="output_format" argument="-f" type="select" multiple="false" label="Output format">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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45 <option value="MAF">MAF</option>
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46 <option value="MAF+" selected="true">MAF+</option>
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47 </param>
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48 <section name="lastsplit_opt" title="Last-split options" expanded="false">
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49 <param argument="-d" type="select" multiple="false" label="RNA direction">
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50 <option value="0">Reverse</option>
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51 <option value="1" selected="true">Forward</option>
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52 <option value="2">Mixed</option>
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53 </param>
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54 <param argument="-c" type="float" value="0.004" label="Cis-splice probability per base"/>
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55 <param argument="-t" type="float" value="0.00001" label="Trans-splice probability per base"/>
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56 <param argument="-M" type="float" value="7" label="Mean of ln[intron length]"/>
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57 <param argument="-S" type="float" value="1.7" label="Standard deviation of ln[intron length]"/>
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58 <param argument="-m" type="float" value="1" label="Maximum mismap probability"/>
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59 <!--<param name="score" argument="-s" type="int" value="lastal e" label="Minimum alignement score"/>-->
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60 <param name="no_split" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Write original, not split, alignement."/>
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61 </section>
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62 </inputs>
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63
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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64 <outputs>
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65 <data name="outfile" format="maf" label="LAST split from ${on_string}" />
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66 </outputs>
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67
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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68 <tests>
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69 <test>
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70 <conditional name="db_opts">
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71 <param name="db_opts_input" value="db"/>
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72 <param name="database" value="humdb"/>
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73 </conditional>
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74 <param name="last_align" ftype="maf" value="last_align_gen.maf"/>
7
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75 <output name="outfile" ftype="maf" file="last_split.maf" lines_diff="2"/>
0
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76 </test>
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77 </tests>
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78
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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79 <help>@LAST_HELP@</help>
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80 <citations><expand macro="citations"/></citations>
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81 </tool>