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"planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
author nml
date Thu, 21 Nov 2019 12:53:20 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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1 <tool id="abacas" name="abacas contig ordering" version="1.1">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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2 <description>Order and Orientate Contigs </description>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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3 <requirements>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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4 <requirement type="package" version="3.23">mummer</requirement>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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5 <requirement type="package" version="5.26.2">perl</requirement>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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6 </requirements>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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7 <command detect_errors="exit_code">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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8 bash '$__tool_directory__/abacas.sh'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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9 '$input_ref'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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10 '$input_query'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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11 '$ordered_contigs'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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12 '$use_bin'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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13 '$non'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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14 '$append_bin'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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15 '$out_bin'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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16 '$out_crunch'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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17 '$out_gaps'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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18 '$out_fasta'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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19 '$out_tab'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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20 '$out_unused'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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21 '$out_multi'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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22 '$out_binmulti'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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23 '$out_nonpseudo'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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24 </command>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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25 <inputs>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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26 <param name="input_ref" type="data" format="fasta" label="Reference sequence" />
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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27 <param name="input_query" type="data" format="fasta" label="Sequence query file"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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28 <param name="ordered_contigs" type="select" format="text" value="yes" label="Generate a multifasta file of the ordered contigs." help="The multifasta file of ordered contigs will be supplemental to the default pseudomolecule fasta file generated.">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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29 <option value="yes">Yes</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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30 <option value="no">No</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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31 </param>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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32 <param name="use_bin" type="select" format="text" value="yes" label="Generate a multifasta file of the unused contigs." help="The unsed contigs refer to contigs that were not used in the alignment.">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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33 <option value="yes">Yes</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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34 <option value="no">No</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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35 </param>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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36 <param name="non" type="select" format="text" value="yes" label="Generate a pseudomolecule by concatenating the aligned contigs without any nnn linkers." help="The no N's fasta file will be supplemental to the default pseudomolecule fasta file generated with n linkers.">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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37 <option value="yes">Yes</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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38 <option value="no">No</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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39 </param>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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40 <param name="append_bin" type="select" format="text" value="yes" label="Append the unused contigs from the bin onto the pseudomolecule." help="The pseudomolecule will be ordered and oriented and then any left over contigs from the bin will be concatenated to the end.">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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41 <option value="yes">Yes</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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42 <option value="no">No</option>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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43 </param>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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44 </inputs>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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45 <outputs>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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46 <data name="out_crunch" format="tabular" label="ACT crunch file"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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47 <data name="out_tab" format="tabular" label="tab files"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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48 <data name="out_gaps" format="tabular" label="gaps file"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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49 <data name="out_fasta" format="tabular" label="pseudmolecule fasta file"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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50 <data name="out_unused" format="tabular" label="unused contig information file"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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51 <data name="out_bin" format="tabular" label="List of unused contigs"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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52 <data name="out_multi" format="fasta" label="Multifasta file of contigs">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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53 <filter>ordered_contigs=="yes"</filter>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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54 </data>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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55 <data name="out_binmulti" format="fasta" label="Multifasta file of bin contigs">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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56 <filter>use_bin=="yes"</filter>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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57 </data>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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58 <data name="out_nonpseudo" format="fasta" label="Pseudomolecule with no N's">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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59 <filter>non=="yes"</filter>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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60 </data>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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61 </outputs>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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62 <tests>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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63 <test>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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64 <param name="input_ref" value="reference_sequence.fasta"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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65 <param name="input_query" value="sequence_query.fasta"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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66 <param name="ordered_contigs" value="no" />
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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67 <param name="use_bin" value="no" />
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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68 <param name="non" value="no" />
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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69 <param name="append_bin" value="no" />
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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70 <output name="out_crunch" value="out_crunch"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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71 <output name="out_tab" value="out_tab"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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72 <output name="out_gaps" value="out_gaps"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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73 <output name="out_fasta" value="out_fasta"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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74 <output name="out_unused" value="out_unused"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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75 <output name="out_bin">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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76 <assert_contents>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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77 <has_text text ="NODE_1_length_1"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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78 <has_text text ="NODE_2_length_10"/>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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79 </assert_contents>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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80 </output>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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81 </test>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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82 </tests>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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83 <help>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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84 <![CDATA[ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence]]>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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85 </help>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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86 <citations>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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87 <citation type="bibtex">
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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88 @misc{sourceforgeABACAS,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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89 title = {ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences},
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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90 publisher = {BioMalPar Consortium and Wellcome Trust Sanger Institute},
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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91 journal = {SourceForge},
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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92 url = {http://abacas.sourceforge.net/index.html},
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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93 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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94 </citation>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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95 </citations>
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
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96 </tool>