Mercurial > repos > peterjc > mummer
annotate tools/mummer/mummer.xml @ 1:b07aa90c95e6 draft
Uploaded v0.0.2, corrects typo on tool ID, adds citation markup.
author | peterjc |
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date | Tue, 28 Oct 2014 06:57:35 -0400 |
parents | b0551f2a5986 |
children | 8f93c1b7609e |
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1
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1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.2"> |
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2 <description>Combine mummer/nucmer/promer with mummerplot</description> |
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3 <requirements> |
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4 <requirement type="binary">ps2pdf</requirement> |
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5 <requirement type="binary">nucmer</requirement> |
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6 <requirement type="binary">mummerplot</requirement> |
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7 <requirement type="package" version="3.23">mummer</requirement> |
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8 </requirements> |
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9 <version_command interpreter="python"> |
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10 mummer.py --version |
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11 </version_command> |
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12 <command interpreter="python"> |
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13 mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output" |
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14 </command> |
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15 <stdio> |
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16 <!-- Anything other than zero is an error --> |
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17 <exit_code range="1:" /> |
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18 <exit_code range=":-1" /> |
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19 </stdio> |
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20 <inputs> |
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21 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> |
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22 <param name="fasta_a" type="data" format="fasta" |
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23 label="Species A" |
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24 description="Nucleotide FASTA file, e.g. contigs from genome assembly." /> |
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25 <param name="fasta_b" type="data" format="fasta" |
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26 label="Species B" |
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27 description="Nucleotide FASTA file, e.g. contigs from genome assembly." /> |
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28 <param name="algorithm" type="select" label="MUMmer search algorithm"> |
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29 <option value="mummer">mummer, efficiently locates maximal unique matches between two sequences</option> |
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30 <option value="nucmer">NUCmer (NUCleotide MUMmer), for closely related sequences</option> |
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31 <option value="promer">PROmer (PROtein MUMmer), using six frame translation of DNA input, for less similar sequences.</option> |
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32 </param> |
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33 <!-- defaults like mincluster vary, 65 for nucmer but 20 for promer --> |
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34 </inputs> |
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35 <outputs> |
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36 <data name="pdf_output" format="pdf" label="$algorithm.value PDF: $fasta_a.name vs $fasta_b.name" /> |
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37 <data name="png_output" format="png" label="$algorithm.value PNG: $fasta_a.name vs $fasta_b.name" /> |
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38 </outputs> |
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39 <requirements> |
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40 </requirements> |
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41 <tests> |
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42 </tests> |
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43 <help> |
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44 **What it does** |
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45 |
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46 Takes two FASTA files (*species A* and *species B*), compares them using one |
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47 of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), checking both |
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48 strands, and then draws a dotplot using ``mummerplot``. |
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49 |
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50 The full MUMmer suite is more flexible and capable than this limited wrapper. |
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51 |
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52 **References** |
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53 |
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54 MUMmer manual: v3.22 http://mummer.sourceforge.net/manual/ |
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55 |
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56 MUMmer tutorials: http://mummer.sourceforge.net/examples/ |
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57 |
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58 If you use MUMmer 3, please cite: |
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59 |
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60 S. Kurtz et al. (2004). |
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61 Versatile and open software for comparing large genomes. |
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62 Genome Biology (2004), 5:R12. |
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63 http://dx.doi.org/10.1186/gb-2004-5-2-r12 |
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64 |
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65 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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66 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mummer |
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67 </help> |
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68 <citations> |
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69 <citation type="doi">10.1186/gb-2004-5-2-r12</citation> |
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70 </citations> |
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71 </tool> |