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annotate README @ 5:3b803b7f3388 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:48:16 -0400
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14062c54b6f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
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14062c54b6f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 The Mothur Tool Suite repository:
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4 - Provides Mothur wrappers for the Mothur tools
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5 - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system
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7 Installing Tools via the API:
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8 This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead
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9 - Install ephemeris: pip install ephemeris -U
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10 - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml
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11 - (You can find a tools.yaml you can use in this repo as well)
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14062c54b6f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 Installing reference data from silva and greengenes:
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14 - There is a Galaxy datamanager for available for Mothur
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16 RDP reference file (modified for mothur):
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17 http://www.mothur.org/wiki/RDP_reference_files
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18 - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
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19 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
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20 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
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21 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
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22 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
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23 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
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24 Silva reference:
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25 http://www.mothur.org/wiki/Silva_reference_files
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26 - Bacterial references (14,956 sequences)
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27 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
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28 - Archaeal references (2,297 sequences)
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29 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
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30 - Eukaryotic references (1,238 sequences)
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31 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
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32 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
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33 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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34 Alignment database rRNA gene sequences:
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35 http://www.mothur.org/wiki/Alignment_database
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36 - greengenes reference alignment
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37 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
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38 - SILVA (Silva reference)
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39 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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40 Secondary structure mapping files:
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41 http://www.mothur.org/wiki/Secondary_structure_map
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42 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
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43 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
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44 Lane masks:
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45 http://www.mothur.org/wiki/Lane_mask
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46 greengenes-compatible mask:
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47 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
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48 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
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49 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
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50 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
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51 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
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52 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
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53 SILVA-compatible mask:
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54 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
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55 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
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56 Lookup Files for sff flow analysis using shhh.flows:
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57 http://www.mothur.org/wiki/Alignment_database