Mercurial > repos > mbernt > data_manager_mitos

annotate data_manager/data_manager_mitos.xml @ 1:7548eaf95697 draft

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"planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
author mbernt
date Sat, 21 Mar 2020 15:32:06 +0000
parents 6d384a5c22bf
children ae5ddc5a6511
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6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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1 <?xml version="1.0"?>
1
7548eaf95697 "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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2 <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2">
0
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3 <description>reference data downloader</description>
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4 <command detect_errors="exit_code">
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5 <![CDATA[
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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6 python '$__tool_directory__/data_manager.py'
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7 --out '${out_file}'
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8 --type '$type_cond.type_select'
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9 --db '$type_cond.database'
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10 ]]>
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11 </command>
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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12 <inputs>
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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13 <conditional name="type_cond">
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14 <param name="type_select" type="select" label="MITOS version">
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15 <option value="mitos">MITOS</option>
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16 <option value="mitos2">MITOS2</option>
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17 </param>
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18 <when value="mitos">
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19 <param name="database" type="select" label="Reference data version">
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20 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
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21 </param>
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22 </when>
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23 <when value="mitos2">
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24 <param name="database" type="select" label="Reference data version">
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25 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
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26 <option value="refseq63m">RefSeq63 Metazoa</option>
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27 <option value="refseq63f">RefSeq63 Fungi</option>
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28 <option value="refseq63o">RefSeq63 Opisthokonta</option>
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29 <option value="refseq89m">RefSeq89 Metazoa</option>
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30 <option value="refseq89f">RefSeq89 Fungi</option>
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31 <option value="refseq89o">RefSeq89 Opisthokonta</option>
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32 </param>
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <outputs>
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37 <data name="out_file" format="data_manager_json" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <conditional name="type_cond">
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42 <param name="type_select" value="mitos"/>
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43 <param name="database" value="mitos1-refdata"/>
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44 </conditional>
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45 <output name="out_file" file="mitos_refseq39.json"/>
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46 </test>
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47 </tests>
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48 <help>
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49 This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
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50
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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51 For MITOS the reference data includes
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52
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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53 - protein data bases derived from RefSeq release 39 (see Bernt et al. 2012)
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54 - covariance models for tRNAs and rRNAs as described in Jühling et al 2012
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55
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56 For MITOS2 the reference data sets are available for three different taxons
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57
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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58 - Metazoa
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59 - Fungi
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60 - Opisthokonta
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61
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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62 these have been computed for RefSeq release 63 and 89. In addition the reference data
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63 for MITOS1 has been converted to be usable in MITOS2.
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64 contains
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65
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66 The reference data sets contain:
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67
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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68 - protein data bases derived from the corresponding RefSeq release Donath et al. 2019
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69 - covariance models computed for the data in the RefSeq releas based on the MITOS1 models
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70 - in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017
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71 </help>
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72 <citations>
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73 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
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74 <citation type="doi">10.1093/nar/gkr1131</citation>
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75 <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
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76 <citation type="doi">10.1093/nar/gkz833</citation>
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77 </citations>
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78 </tool>
6d384a5c22bf "planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"
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