Mercurial > repos > galaxyp > data_manager_eggnog_mapper

annotate data_manager/eggnog_macros.xml @ 3:5a2ffc486246 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
author galaxyp
date Tue, 25 Jan 2022 13:50:50 +0000
parents 3d82020b1e3b
children 516eb4e1cf8e
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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1 <?xml version="1.0"?>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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2 <macros>
3
5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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3 <token name="@VERSION@">2.1.6</token>
5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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4 <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
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3d82020b1e3b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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5 <!--
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5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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6 # DB versionning was super confusing for eggnog-mapper 2.0.x:
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3d82020b1e3b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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7 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
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5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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8 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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9 # (db v4.5 are not compatible with eggnog-mapper 2.0)
5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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10 # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
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3d82020b1e3b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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11 -->
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5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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12 <token name="@IDX_VERSION@">5.0.2</token>
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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13 <xml name="citations">
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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14 <citations>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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15 <citation type="doi">10.1093/nar/gkv1248</citation>
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077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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16 <citation type="doi">10.1093/molbev/msx148</citation>
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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17 </citations>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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18 </xml>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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19 <xml name="requirements">
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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20 <requirements>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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21 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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22 </requirements>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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23 </xml>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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24 <xml name="version_command">
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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25 <version_command>emapper.py --version</version_command>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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26 </xml>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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27 <xml name="data_manager_params">
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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28 <param name="test" type="hidden" value="false" />
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29 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/>
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30 <param name="mmseqs_database" type="boolean" truevalue="-M" falsevalue="" checked="true" label="Install the MMseqs2 database" help="Required for mmseqs seed ortholog search mode. Takes ~11Gb, you most probably want it."/>
5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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31 <param name="pfam_database" type="boolean" truevalue="-P" falsevalue="" checked="true" label="Install the Pfam database" help="Rquired for de novo annotation or realignment. Takes ~3Gb, you most probably want it."/>
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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32 </xml>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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33 <xml name="data_manager_outputs">
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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34 <outputs>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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35 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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36 </outputs>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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37 </xml>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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38 <token name="@DOWNLOAD_CMD@"><![CDATA[
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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39 ## tool should set install_path
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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40 #if $test == 'true'
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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41 #import os.path
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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42 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
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43 #end if
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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44 mkdir -p '${install_path}' &&
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45 download_eggnog_data.py
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46 $diamond_database $mmseqs_database $pfam_database -y -q
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47 #if $test == 'true'
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48 -s
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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49 #end if
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50 --data_dir '$install_path' &&
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51 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path'
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52 ]]></token>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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53 <xml name="data_manager_test">
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54 <test>
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55 <param name="test" value="true"/>
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56 <param name="diamond_database" value="true"/>
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57 <yield />
0
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58 <output name="out_file">
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59 <assert_contents>
2
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60 <has_text text="eggnog_mapper_db_versioned" />
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61 <has_text text="@EGGNOG_DB_VERSION@" />
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62 </assert_contents>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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63 </output>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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64 </test>
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65 </xml>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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66 </macros>