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annotate cap3.xml @ 0:d76a0d8a9eac draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
author artbio
date Sat, 02 Sep 2017 07:09:11 -0400
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d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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1 <tool id="cap3" name="cap3" version="2.0.0">
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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2 <description>Sequence Assembly tool</description>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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3 <requirements>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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4 <requirement type="package" version="10.2011">cap3</requirement>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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5 </requirements>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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10 cap3 "$inputSequences" -o $overlaplength -p $overlapidentity > "$cap3stdout" &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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11 mv "$inputSequences".cap.contigs $contigs &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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12 mv "$inputSequences".cap.contigs.qual $contigsqual &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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13 mv "$inputSequences".cap.contigs.links $contigslink &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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14 mv "$inputSequences".cap.ace $ace &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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15 mv "$inputSequences".cap.info $info &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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16 mv "$inputSequences".cap.singlets $singlets &&
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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17 cat $contigs $singlets > $contigsandsinglets
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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18 ]]></command>
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19
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20 <inputs>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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21 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
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22 <param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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23 <param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90" help="-p option. must be > 65. 90 by default" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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24 </inputs>
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25
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26 <outputs>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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27 <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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28 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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29 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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30 <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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31 <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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32 <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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33 <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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34 <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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35 </outputs>
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36
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37 <tests>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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38 <test>
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39 <param name="inputSequences" value="input.fa" ftype="fasta"/>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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40 <param name="overlaplength" value="40" />
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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41 <param name="overlapidentity" value="90" />
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42 <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
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43 <output name="cap3stdout" file="cap3stdout.txt"/>
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44 <output name="contigs" file="contigs.fa"/>
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45 <output name="contigsqual" file="contigsqual.txt"/>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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46 <output name="contigslink" file="contigslink.txt"/>
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47 <output name="ace" file="ace.txt"/>
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48 <output name="info" file="info.txt"/>
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49 <output name="singlets" file="singlets.fa"/>
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50 </test>
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51 </tests>
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52
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d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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54 <help>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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55 **What it does**
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56
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57 This tool is a CAP3 wrapper developed for the visitor2 set of worflows
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58
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59 Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences
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d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
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61 Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets).
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62
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63 Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)
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64
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65 **Acknowledgments**
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66
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67 This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson.
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68
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69 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
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70
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71 .. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
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72 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
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73 .. _MIT license: http://opensource.org/licenses/MIT
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74
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75
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76 </help>
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77 <citations>
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78 <citation type="bibtex">@article{Huang:1999wb,
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79 author = {Huang, X and Madan, A},
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80 title = {{CAP3: A DNA sequence assembly program.}},
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81 journal = {Genome research},
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82 year = {1999},
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83 volume = {9},
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
diff changeset
84 number = {9},
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
diff changeset
85 pages = {868--877},
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
diff changeset
86 month = sep
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
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87 }
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
diff changeset
88 </citation>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
diff changeset
89 </citations>
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
diff changeset
90
d76a0d8a9eac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a
artbio
parents:
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91 </tool>