Mercurial > repos > galaxyp > eggnog_mapper
annotate eggnog_macros.xml @ 6:3cb37af59360 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author | galaxyp |
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date | Sat, 05 Sep 2020 07:21:28 +0000 |
parents | a5a3bdd0954b |
children | 4e4c6329f6cd |
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a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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1 <?xml version="1.0"?> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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2 <macros> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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3 <token name="@VERSION@">2.0.1</token> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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4 <token name="@EGGNOG_DB_VERSION@">5.0</token> |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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5 <xml name="citations"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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6 <citations> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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7 <citation type="doi">10.1093/nar/gkv1248</citation> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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8 <citation type="doi">10.1093/molbev/msx148</citation> |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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9 </citations> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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10 </xml> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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11 <xml name="requirements"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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12 <requirements> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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13 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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14 </requirements> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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15 </xml> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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16 <xml name="version_command"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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17 <version_command>emapper.py --version</version_command> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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18 </xml> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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19 <xml name="data_manager_params"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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20 <param name="test" type="hidden" value="false" /> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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21 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/> |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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22 </xml> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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23 <xml name="data_manager_outputs"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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24 <outputs> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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25 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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26 </outputs> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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27 </xml> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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28 <token name="@DOWNLOAD_CMD@"><![CDATA[ |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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29 ## tool should set install_path |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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30 #if $test == 'true' |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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31 #import os.path |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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32 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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33 #end if |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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34 mkdir -p '${install_path}' && |
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3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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35 download_eggnog_data.py |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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36 $diamond_database -y -q |
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a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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37 #if $test == 'true' |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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38 -s |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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39 #end if |
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3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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40 --data_dir '$install_path' && |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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41 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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42 ]]></token> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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43 <xml name="data_manager_test"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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44 <test> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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45 <param name="test" value="true"/> |
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3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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46 <param name="diamond_database" value="true"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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47 <yield /> |
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a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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48 <output name="out_file"> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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49 <assert_contents> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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50 <has_text text="eggnog_mapper_db" /> |
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3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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51 <has_text text="@EGGNOG_DB_VERSION@" /> |
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a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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52 </assert_contents> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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53 </output> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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54 </test> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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55 </xml> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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56 </macros> |