Mercurial > repos > iuc > data_manager_mitos

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:36:28 +0000
parents 19d9be08560c
children
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26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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1 <?xml version="1.0"?>
4
d9339bb8127e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit a54e50916ebdb0858b049cdc549a43df801e1a71
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2 <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.3" profile="23.0">
0
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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3 <description>reference data downloader</description>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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4 <requirements>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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5 <requirement type="package" version="3.7">python</requirement>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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6 </requirements>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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7 <command detect_errors="exit_code">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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8 <![CDATA[
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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9 python '$__tool_directory__/data_manager.py'
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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10 --out '${out_file}'
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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11 --type '$type_cond.type_select'
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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12 --db '$type_cond.database'
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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13 ]]>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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14 </command>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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15 <inputs>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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16 <conditional name="type_cond">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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17 <param name="type_select" type="select" label="MITOS version">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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18 <option value="mitos">MITOS</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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19 <option value="mitos2">MITOS2</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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20 </param>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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21 <when value="mitos">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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22 <param name="database" type="select" label="Reference data version">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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23 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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24 </param>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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25 </when>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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26 <when value="mitos2">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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27 <param name="database" type="select" label="Reference data version">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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28 <option value="refseq63m">RefSeq63 Metazoa</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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29 <option value="refseq63f">RefSeq63 Fungi</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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30 <option value="refseq63o">RefSeq63 Opisthokonta</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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31 <option value="refseq89m">RefSeq89 Metazoa</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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32 <option value="refseq89f">RefSeq89 Fungi</option>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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33 <option value="refseq89o">RefSeq89 Opisthokonta</option>
2
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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34 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
0
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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35 </param>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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36 </when>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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37 </conditional>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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38 </inputs>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39 <outputs>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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40 <data name="out_file" format="data_manager_json" />
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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41 </outputs>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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42 <tests>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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43 <test>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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44 <conditional name="type_cond">
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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45 <param name="type_select" value="mitos"/>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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46 <param name="database" value="mitos1-refdata"/>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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47 </conditional>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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48 <output name="out_file" file="mitos_refseq39.json"/>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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49 </test>
2
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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50 <test>
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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51 <conditional name="type_cond">
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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52 <param name="type_select" value="mitos2"/>
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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53 <param name="database" value="refseq63m"/>
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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54 </conditional>
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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55 <output name="out_file" file="mitos2_refseq63.json"/>
19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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56 </test>
0
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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57 </tests>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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58 <help>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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59 This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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60
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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61 For MITOS the reference data includes
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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62
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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63 - protein data bases derived from RefSeq release 39 (see Bernt et al. 2012)
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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64 - covariance models for tRNAs and rRNAs as described in Jühling et al 2012
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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65
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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66 Data is downloaded from https://zenodo.org/record/2683856.
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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67
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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68 For MITOS2 the reference data sets are available for three different taxons
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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69
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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70 - Metazoa
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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71 - Fungi
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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72 - Opisthokonta
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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73
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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74 these have been computed for RefSeq release 63 and 89. In addition the reference data
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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75 for MITOS1 has been converted to be usable in MITOS2.
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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76 contains
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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77
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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78 The reference data sets contain:
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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79
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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80 - protein data bases derived from the corresponding RefSeq release Donath et al. 2019
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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81 - covariance models computed for the data in the RefSeq releas based on the MITOS1 models
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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82 - in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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83
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19d9be08560c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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84 Data is downloaded from https://zenodo.org/record/4284483.
0
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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85 </help>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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86 <citations>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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87 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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88 <citation type="doi">10.1093/nar/gkr1131</citation>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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89 <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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90 <citation type="doi">10.1093/nar/gkz833</citation>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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91 </citations>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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92 </tool>
26a6f95e82c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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93