Mercurial > repos > nml > mauve_contig_mover

annotate mauve_contig_mover.xml @ 0:b8bc1922226a draft default tip

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"planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
author nml
date Thu, 21 Nov 2019 12:37:56 -0500
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0
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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1 <tool id="mauve_contig_mover" name="Mauve Contig Mover" version="1.0.10">
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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2 <description>MCM can be used to order a draft genome relative to a related reference genome.</description>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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3 <requirements>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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4 <requirement type="package" version="2.4.0.r4736">mauve</requirement>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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5 <requirement type="package" version="3.23">mummer</requirement>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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6 <requirement type="package" version="1.3.1=h470a237_0">libgenome</requirement>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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7 <requirement type="package" version="snapshot_2015_02_13">progressivemauve</requirement>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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8 </requirements>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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9 <command detect_errors="exit_code">
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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10 <![CDATA[
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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11 export path2jar=`find \$JAVA_HOME -name 'Mauve.jar'` &&
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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12 perl '$__tool_directory__/mauve_contig_mover.pl'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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13 -r '$reference'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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14 -d '$draft'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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15 -o '$html_file.files_path'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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16 -a '$alignment_file'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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17 -f '$fasta_file'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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18 -l '$html_file'
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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19 ]]>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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20 </command>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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21 <inputs>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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22 <param name="reference" type="data" format="fasta,genbank" label="Reference Sequence"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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23 <param name="draft" type="data" format="fasta" label="Draft Genome"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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24 <param name="output" size="30" type="text" value="output" label="Please specify a name for the output files" />
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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25 </inputs>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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26 <outputs>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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27 <data name="html_file" format="html" label="${output}_mauve_summary.html" />
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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28 <data name="alignment_file" format="text" label="${output}_alignment" />
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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29 <data name="fasta_file" format="fasta" label="${output}.fasta" />
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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30 </outputs>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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31
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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32
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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33
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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34
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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35 <tests>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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36 <test>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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37 <param name="reference" value="reference.gbk"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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38 <param name="draft" value="draft.fasta"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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39 <param name="output" value="output" />
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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40 <output name="fasta_file" value="output.fasta"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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41 <output name="html_file" value="output.html"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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42 <output name="alignment_file">
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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43 <assert_contents>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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44 <has_text text="> 1:1-150297 + "/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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45 <has_text text="atggtcaaaggtgcgagaaggataatggtgcaggccacaagctctagtgctggcaagacgcttctgtgtttgtgtttgtg"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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46 <has_text text="> 2:0-0 +"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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47 <has_text text="--------------------------------------------------------------------------------"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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48 <has_text text="> 2:1-275 +"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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49 <has_text text="gatacaaaaaccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagggggggggggggggggggg"/>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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50 </assert_contents>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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51 </output>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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52
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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53 </test>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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54 </tests>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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55 <help>
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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56 **What it does**
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57 The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to a reference genome. In many cases, true rearrangements in the draft relative to the reference can be identified. The quality of the reorder is limited by the distance between the sequences, as indicated by the amount of shared gene content among the two organisms. A more distant reference will usually yield fewer ordered draft genome contigs, and may also induce erroneous placements of draft contigs. In addition to ordering contigs, MCM also orient them in the most likely orientation, and, if annotated sequence features are specified in an input file (e.g. with GenBank format input for the draft), MCM will output adjusted coordinates ranges for the features In many cases, true rearrangements in the draft relative to the reference can be identified. The quality of the reorder is limited by the distance between the sequences, as indicated by the amount of shared gene content among the two organisms. A more distant reference will usually yield fewer ordered draft genome contigs, and may also induce erroneous placements of draft contigs. In addition to ordering contigs, MCM also orient them in the most likely orientation, and, if annotated sequence features are specified in an input file (e.g. with GenBank format input for the draft), MCM will output adjusted coordinates ranges for the features.
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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58 For more information, visit http://asap.ahabs.wisc.edu/mauve/index.php
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59
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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60
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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61 **Input Formats**
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62
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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63 -- Reference Sequence: Enter a genbank or fasta file containing the reference sequence.
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64
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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65 -- Draft Genome: Enter a fasta file containing the draft genome to reorder.
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66
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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67
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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68 **Output**
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69
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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70 This tool will give you three output files:
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71
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72 -- Fasta file: Contains the ordered contigs according to the last alignment done by Mauve
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73
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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74 -- Alignment file: An XMFA file. This file can be opened using the Mauve Graphical Interface
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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75
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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76 -- HTML file: A summary of the alignments performed by Mauve. Downloading the contents of this file will give a zip file containing the Mauve output folder.
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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77
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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78 </help>
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79
b8bc1922226a "planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
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80 </tool>