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1 motif_tools
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2 ===========
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3
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4 Galaxy tools for various motif-finding utilities developed by Ian Donaldson.
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5
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6 There are five tools available:
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7
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8 * **IUPAC scan and output each match** Returns all matches to a given IUPAC in
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9 GFF format
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10
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11 * **IUPAC scan and output matches per seq** Counts the matches to a given IUPAC
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12
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13 * **Count unique seq in GFF** Gives the non-redundant count of sequences
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14
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15 * **TFBScluster two TFBS** Identifies clusters of two TFBS
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16
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17 * **TFBScluster three TFBS** Identifies clusters of three TFBS
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18
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19 Automated installation
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20 ======================
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21
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22 Installation via the Galaxy Tool Shed will take of installing the tools
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23 and the underlying dependencies.
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24
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25 Manual Installation
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26 ===================
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27
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28 To add these to Galaxy put the following lines in tool_conf.xml for each:
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29 tool that you want::
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30
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31 <tool file="motif_tools/Scan_IUPAC_output_each_match.xml" />
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32 <tool file="motif_tools/Scan_IUPAC_output_matches_per_seq.xml" />
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33 <tool file="motif_tools/CountUniqueIDs.xml" />
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34 <tool file="motif_tools/TFBScluster_candidates_2TFBS.xml" />
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35 <tool file="motif_tools/TFBScluster_candidates_3TFBS.xml" />
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36
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37 The tools also require Perl and ``Bioperl`` to be installed.
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38
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39 History
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40 =======
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41
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42 ========== =====================================================================
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43 =
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44 Version Changes
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45 ---------- ----------------------------------------------------------------------
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46 - 1.0.1 Updates to use conda dependency resolution and tidy up XML
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47 - 1.0.0 Initial version
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48 ========== =====================================================================
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49 =
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50
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51 Developers
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52 ==========
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53
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54 This tool is developed on the following GitHub repository:
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55 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/tools/macs21
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56
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57
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58 Licence (MIT)
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59 =============
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60
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61 Permission is hereby granted, free of charge, to any person obtaining a copy
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62 of this software and associated documentation files (the "Software"), to deal
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63 in the Software without restriction, including without limitation the rights
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64 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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65 copies of the Software, and to permit persons to whom the Software is
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66 furnished to do so, subject to the following conditions:
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67
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68 The above copyright notice and this permission notice shall be included in
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69 all copies or substantial portions of the Software.
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70
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71 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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72 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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73 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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74 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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75 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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76 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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77 THE SOFTWARE.
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