Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_macros.xml @ 14:d9c3016f7283 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 192779247c3385704ebd98a2cc47a210fb1f4d0c
author galaxyp
date Thu, 07 Sep 2023 18:51:23 +0000
parents 844fa988236b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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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"
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2 <macros>
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5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
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3 <token name="@TOOL_VERSION@">2.1.8</token>
14
d9c3016f7283 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 192779247c3385704ebd98a2cc47a210fb1f4d0c
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4 <token name="@VERSION_SUFFIX@">4</token>
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96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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5 <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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6 <token name="@PROFILE@">22.01</token>
7
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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7 <!--
8
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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8 # DB versionning was super confusing for eggnog-mapper 2.0.x:
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4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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9 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
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96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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10 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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11 # (db v4.5 are not compatible with eggnog-mapper 2.0)
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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12 # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
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4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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13 -->
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96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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14 <token name="@IDX_VERSION@">5.0.2</token>
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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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15 <xml name="citations">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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16 <citations>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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17 <citation type="doi">10.1093/nar/gkv1248</citation>
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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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18 <citation type="doi">10.1093/molbev/msx148</citation>
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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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19 </citations>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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20 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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21 <xml name="requirements">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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22 <requirements>
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5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
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23 <requirement type="package" version="@TOOL_VERSION@">eggnog-mapper</requirement>
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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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24 </requirements>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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25 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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26 <xml name="version_command">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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27 <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"
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28 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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29 <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"
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30 <param name="test" type="hidden" value="false" />
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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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31 <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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96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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32 <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."/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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33 <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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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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34 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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35 <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"
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36 <outputs>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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37 <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"
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38 </outputs>
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 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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40 <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"
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41 ## 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"
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42 #if $test == 'true'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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43 #import os.path
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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44 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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45 #end if
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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46 mkdir -p '${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"
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47 download_eggnog_data.py
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96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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48 $diamond_database $mmseqs_database $pfam_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"
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49 #if $test == 'true'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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50 -s
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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51 #end if
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3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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52 --data_dir '$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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53 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path'
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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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54 ]]></token>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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55 <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"
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56 <test>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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57 <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"
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58 <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"
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59 <yield />
5
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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60 <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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61 <assert_contents>
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4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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62 <has_text text="eggnog_mapper_db_versioned" />
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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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63 <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"
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64 </assert_contents>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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65 </output>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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66 </test>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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67 </xml>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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68
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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69
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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70 <xml name="stdout_assertion">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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71 <assert_stdout>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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72 <has_line line="# emapper-@TOOL_VERSION@"/>
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73 <has_line line="FINISHED"/>
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74 <yield/>
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75 </assert_stdout>
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76 </xml>
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77 <xml name="db_macro">
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78 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
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79 <options from_data_table="eggnog_mapper_db_versioned">
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80 <filter type="static_value" column="3" value="@IDX_VERSION@" />
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81 </options>
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82 </param>
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83 </xml>
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84 <token name="@DB_TOKEN@"><![CDATA[
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85 --data_dir '$eggnog_data.fields.path'
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86 ]]></token>
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87
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88 <!-- macros and tokens for search -->
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89
12
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90 <xml name="fasta_input">
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91 <param argument="-i" name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
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92 <conditional name="input_trans">
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93 <param argument="--itype" type="select" label="Type of sequences">
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94 <option value="proteins" selected="true">proteins</option>
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95 <option value="CDS">CDS</option>
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96 <option value="genome">genome</option>
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97 <option value="metagenome">metagenome</option>
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98 </param>
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99 <when value="proteins"/>
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100 <when value="CDS">
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101 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
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102 label="Translate CDS to proteins before search"/>
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103 </when>
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104 <when value="genome">
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105 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
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106 label="Translate predicted CDS from blastx hits to proteins"/>
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107 <param argument="--genepred" type="select" label="Type of sequences">
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108 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
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109 <option value="prodigal" selected="true">Performed using Prodigal</option>
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110 </param>
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111 </when>
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112 <when value="metagenome">
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113 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
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114 label="Translate predicted CDS from blastx hits to proteins"/>
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115 <param argument="--genepred" type="select" label="Type of sequences">
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116 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
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117 <option value="prodigal" selected="true">Performed using Prodigal</option>
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118 </param>
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119 </when>
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120 </conditional>
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121 </xml>
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122 <!-- Common options for search filtering (applies to diamond and mmseqs only) -->
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123 <xml name="common_search_options">
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124 <param argument="--query_cover" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
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125 <param argument="--subject_cover" type="integer" optional="true" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
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126 <param argument="--pident" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of identity" />
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127 <param argument="--evalue" type="float" optional="true" min="0" label="Minimum query coverage" help="Report only alignments below or equal the e-value" />
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128 <param argument="--score" type="float" value="0.001" optional="true" min="0" label="Minimum query coverage" help="Report only alignments above or equal the score" />
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129 </xml>
13
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130
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131 <xml name="ortho_macro">
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132 <conditional name="ortho_method">
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133 <param argument="-m" type="select" label="Basis for annotation">
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134 <yield name="search_options"/>
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135 <yield name="reuse_options"/>
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136 </param>
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137 <yield name="search_whens"/>
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138 <yield name="reuse_whens"/>
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139 </conditional>
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140 </xml>
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141
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142 <xml name="ortho_search_macro">
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143 <expand macro="ortho_macro">
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144 <token name="search_options">
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145 <expand macro="search_options_macro"/>
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146 </token>
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147 <token name="search_whens">
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148 <expand macro="search_whens_macro"/>
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149 </token>
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150 </expand>
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151 </xml>
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152
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153 <xml name="ortho_annotate_macro">
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154 <expand macro="ortho_macro">
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155 <token name="reuse_options">
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156 <expand macro="reuse_options_macro"/>
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157 </token>
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158 <token name="reuse_whens">
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159 <expand macro="reuse_whens_macro"/>
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160 </token>
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161 </expand>
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162 </xml>
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163
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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164 <xml name="ortho_full_macro">
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165 <expand macro="ortho_macro">
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166 <token name="search_options">
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167 <expand macro="search_options_macro"/>
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168 </token>
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169 <token name="reuse_options">
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170 <expand macro="reuse_options_macro"/>
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171 </token>
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172 <token name="search_whens">
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173 <expand macro="search_whens_macro"/>
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174 </token>
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175 <token name="reuse_whens">
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176 <expand macro="reuse_whens_macro"/>
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177 </token>
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178 </expand>
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179 </xml>
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180
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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181 <xml name="search_options_macro">
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182 <option value="diamond">Seed orthologs computed with Diamond (diamond)</option>
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183 <option value="mmseqs">Seed orthologs computed with MMseqs2 (mmseqs)</option>
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184 </xml>
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185
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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186 <xml name="reuse_options_macro">
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187 <option value="no_search">Use existing seed orthologs (no_search)</option>
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188 <option value="cache">Use cached annotations (cache). See also --md5</option>
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189 </xml>
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190
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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191 <xml name="search_whens_macro">
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192 <when value="diamond">
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193 <expand macro="fasta_input"/>
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194 <conditional name="matrix_gapcosts">
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195 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
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196 <option value="BLOSUM90">BLOSUM90</option>
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197 <option value="BLOSUM80">BLOSUM80</option>
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198 <option value="BLOSUM62" selected="true">BLOSUM62</option>
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199 <option value="BLOSUM50">BLOSUM50</option>
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200 <option value="BLOSUM45">BLOSUM45</option>
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201 <option value="PAM250">PAM250</option>
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202 <option value="PAM70">PAM70</option>
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203 <option value="PAM30">PAM30</option>
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204 </param>
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205 <when value="BLOSUM90">
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206 <param name="gap_costs" type="select" label="Gap Costs">
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207 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
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208 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
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209 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
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210 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
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211 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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212 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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213 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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214 </param>
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215 </when>
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216 <when value="BLOSUM80">
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217 <param name="gap_costs" type="select" label="Gap Costs">
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218 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
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219 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
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220 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
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221 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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222 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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223 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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224 </param>
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225 </when>
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226 <when value="BLOSUM62">
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227 <param name="gap_costs" type="select" label="Gap Costs">
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228 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
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diff changeset
229 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
230 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
231 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
232 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
233 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
234 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
235 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
236 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
237 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
238 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
239 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
240 </when>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
241 <when value="BLOSUM50">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
242 <param name="gap_costs" type="select" label="Gap Costs">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
243 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
244 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
245 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
246 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
247 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
248 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
249 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
250 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
251 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
252 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
253 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
254 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
255 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
256 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
257 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
258 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
259 </when>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
260 <when value="BLOSUM45">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
261 <param name="gap_costs" type="select" label="Gap Costs">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
262 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
263 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
264 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
265 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
266 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
267 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
268 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
269 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
270 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
271 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
272 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
273 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
274 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
275 </when>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
276 <when value="PAM250">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
277 <param name="gap_costs" type="select" label="Gap Costs">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
278 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
279 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
280 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
281 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
282 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
283 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
284 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
285 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
286 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
287 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
288 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
289 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
290 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
291 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
292 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
293 </when>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
294 <when value="PAM70">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
295 <param name="gap_costs" type="select" label="Gap Costs">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
296 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
297 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
298 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
299 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
300 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
301 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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302 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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303 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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304 </param>
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305 </when>
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306 <when value="PAM30">
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307 <param name="gap_costs" type="select" label="Gap Costs">
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308 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
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309 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
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310 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
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311 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
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312 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
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313 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
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314 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
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315 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
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316 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
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317 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
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318 </param>
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319 </when>
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320 </conditional>
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321 <param argument="--sensmode" type="select" label="Diamond's sensitivity mode">
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322 <option value="default">default</option>
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323 <option value="fast">fast</option>
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324 <option value="mid-sensitive">mid-sensitive</option>
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325 <option value="sensitive" selected="true">sensitive</option>
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326 <option value="more-sensitive">more-sensitive</option>
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327 <option value="very-sensitive">very-sensitive</option>
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328 <option value="ultra-sensitive">ultra-sensitive</option>
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329 </param>
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330 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false"
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331 label="Run diamond in iterative mode, up to the sensitivity level"/>
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332 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false"
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333 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/>
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334 <expand macro="common_search_options"/>
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335 </when>
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336 <when value="mmseqs">
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337 <expand macro="fasta_input"/>
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338 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" />
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339 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" />
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340 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" />
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341 <expand macro="common_search_options"/>
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342 </when>
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343 </xml>
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344
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345 <xml name="reuse_whens_macro">
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346 <when value="no_search">
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347 <param argument="--annotate_hits_table" type="data" multiple="true" format="tabular" label="Seed orthologs">
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348 <validator type="expression" message="No seed orthologs">value.metadata.columns == 11</validator>
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349 <!-- would be cool to replace with this validator:
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350 <validator type="expression" message="No seed orthologs">value.metadata.column_names == '@SEED_ORTHOLOG_COLUMNS@'.split()</validator>
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351 but this does not work (yet) in tool tests since column_names can not be set in uploads -->
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352 </param>
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353 </when>
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354 <when value="cache">
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355 <expand macro="fasta_input"/>
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356 <param argument="--cache" type="data" format="tabular" label="EggNOG Annotations with md5 hashes" help="Annotations computed with EggNOG mapper with enabled --md5 option">
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357 <validator type="expression" message="No seed orthologs">value.metadata.columns == 22</validator>
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358 </param>
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359 <param name="output_no_annotations" type="boolean" checked="true" label="Output sequences without annotation" help="Produce an additional FASTA file with the sequences of queries for which an existing annotation was not found using cache mode. This file can be used as input of another eggNOG-mapper run without using the cache, trying to annotate the sequences."/>
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360 </when>
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361 </xml>
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362
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363 <token name="@MERGE_ANNOTATIONS@"><![CDATA[
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364 #if $ortho_method.m == "no_search"
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365 cat
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366 #for aht in $ortho_method.annotate_hits_table
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367 $aht
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368 #end for
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369 > annotate_hits_table.tsv
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370 &&
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371 #end if
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372 ]]></token>
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373
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374 <token name="@ORTHO_SEARCH_TOKEN@"><![CDATA[
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375 -m '$ortho_method.m'
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376 #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']:
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377 -i '$ortho_method.input'
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378 --itype '$ortho_method.input_trans.itype'
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379 #if $ortho_method.input_trans.itype in ['CDS', 'genome', 'metagenome']:
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diff changeset
380 $ortho_method.input_trans.translate
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381 #end if
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382 #if $ortho_method.input_trans.itype in ['genome', 'metagenome']:
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383 --genepred $ortho_method.input_trans.genepred
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384 #end if
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diff changeset
385 #elif $ortho_method.m == "no_search"
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386 --annotate_hits_table annotate_hits_table.tsv
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387 #end if
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diff changeset
388
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
389 #if $ortho_method.m == 'cache'
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390 --cache '$ortho_method.cache'
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391 #end if
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392 #if $ortho_method.m == 'no_search'
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393 --annotate_hits_table annotate_hits_table.tsv
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394 #end if
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395
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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396 #if $ortho_method.m in ['diamond', 'mmseqs']:
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397 ## Diamond option
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398 #if $ortho_method.m == "diamond":
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399 --matrix '$ortho_method.matrix_gapcosts.matrix'
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
400 $ortho_method.matrix_gapcosts.gap_costs
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diff changeset
401 --sensmode $ortho_method.sensmode
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
402 $ortho_method.dmnd_iterate
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
403 $ortho_method.dmnd_ignore_warnings
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
404 #elif $ortho_method.m == "mmseqs":
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
405 --start_sens $ortho_method.start_sens
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
406 --sens_steps $ortho_method.sens_steps
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
407 --final_sens $ortho_method.final_sens
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
408 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
409
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
410 ## Common options for search filtering (applies to diamond and mmseqs only)
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
411 #if str($ortho_method.query_cover):
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
412 --query_cover $ortho_method.query_cover
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
413 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
414 #if str($ortho_method.subject_cover):
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galaxyp
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415 --subject_cover $ortho_method.subject_cover
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
416 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
417 #if str($ortho_method.pident):
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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418 --pident $ortho_method.pident
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419 #end if
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diff changeset
420 #if str($ortho_method.evalue):
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diff changeset
421 --evalue $ortho_method.evalue
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diff changeset
422 #end if
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diff changeset
423 #if str($ortho_method.score):
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
424 --score $ortho_method.score
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diff changeset
425 #end if
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diff changeset
426 #end if
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diff changeset
427 ]]></token>
12
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diff changeset
428
13
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diff changeset
429 <!-- output options applying to search step -->
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diff changeset
430 <xml name="output_options_macro">
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431 <section name="output_options" expanded="false" title="Output Options">
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432 <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
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diff changeset
433 label="Exclude header lines and stats from output files"/>
12
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434 <yield/>
13
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435 </section>
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diff changeset
436 </xml>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
437 <!-- output options applying search and annotate step -->
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diff changeset
438 <xml name="output_options_annotate_macro">
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diff changeset
439 <expand macro="output_options_macro">
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440 <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" label="Output a file with the list of orthologs for each hit"/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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441 <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false" label="Add md5 hash of each query to annotations"/>
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diff changeset
442 </expand>
11
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diff changeset
443 </xml>
13
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diff changeset
444
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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445 <token name="@SEED_ORTHOLOG_COLUMNS@">query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov</token>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
446
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
447 <xml name="ortho_search_output_macro">
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diff changeset
448 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
449 <filter>ortho_method['m'] not in ['no_search', 'cache']</filter>
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diff changeset
450 <actions>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
451 <action name="column_names" type="metadata" default="@SEED_ORTHOLOG_COLUMNS@"/>
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diff changeset
452 </actions>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
453 </data>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
454 </xml>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
455
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
456 <xml name="seed_orthologs_assertion" token_nocomments="true">
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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457 <output name="seed_orthologs" ftype="tabular">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
458 <assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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459 <has_line line="#qseqid&#009;sseqid&#009;evalue&#009;bitscore&#009;qstart&#009;qend&#009;sstart&#009;send&#009;pident&#009;qcov&#009;scov"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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460 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\d+){4}(\t[.\d]+){3}" n="1"/>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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461 <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
462 </assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
463 </output>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
464 </xml>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
465
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
466 <token name="@HELP_SEARCH_OUTPUTS@"><![CDATA[
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
467 **seed orthologs**
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
468
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
469 each line in the file provides the best match of each query within the best Orthologous Group (OG)
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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470 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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471 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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472 If using the diamond search mode, seed orthologs are directly
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
473 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
474 ]]></token>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
475
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
476 <!-- macros and tokens for annotate -->
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
477
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
478 <xml name="annotation_options_macro">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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479 <param argument="--seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
480 <help>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
481 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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482 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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483 </help>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
484 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
485 <param argument="--seed_ortholog_score" type="float" optional="true" min="0" label="Minimum bit score threshold">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
486 <help>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
487 Min bit score expected when searching for seed eggNOG ortholog.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
488 Queries not having a significant seed orthologs will not be annotated.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
489 </help>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
490 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
491 <param argument="--tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
492 <param argument="--target_orthologs" type="select" label="target orthologs for functional transfer">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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493 <option value="one2one">one2one</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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494 <option value="many2one">many2one</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
495 <option value="one2many">one2many</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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496 <option value="many2many">many2many</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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497 <option value="all" selected="true">all</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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498 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
499 <param argument="--go_evidence" type="select"
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
500 label="Select the set of GO terms that should be used for annotation">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
501 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
502 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
503 <option value="all" selected="true">All (experimental + non-electronic)</option>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
504 </param>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
505 </xml>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
506 <token name="@ANNOTATION_TOKEN@"><![CDATA[
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
507 #if str($annotation_options.seed_ortholog_evalue):
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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508 --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue
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diff changeset
509 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
510 #if str($annotation_options.seed_ortholog_score):
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
511 --seed_ortholog_score $annotation_options.seed_ortholog_score
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
512 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
513 #if $annotation_options.tax_scope:
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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514 --tax_scope=$annotation_options.tax_scope
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
515 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
516 #if $annotation_options.target_orthologs:
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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517 --target_orthologs=$annotation_options.target_orthologs
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
518 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
519 #if $annotation_options.go_evidence:
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
520 --go_evidence=$annotation_options.go_evidence
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
521 #end if
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
522 \$EGGNOG_DBMEM
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
523 ]]></token>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
524 <xml name="annotation_output_macro">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
525 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
526 <yield/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
527 <actions>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
528 <conditional name="output_options.md5">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
529 <when value="True">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
530 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
531 </when>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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diff changeset
532 <when value="False">
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
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533 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
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diff changeset
534 </when>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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535 </conditional>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
536 </actions>
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537 </data>
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538 <data name="no_annotations" format="fasta" label="${tool.name} on ${on_string}: sequences without annotation" from_work_dir="results.emapper.no_annotations.fasta">
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539 <filter>ortho_method['m'] == 'cache' and ortho_method['output_no_annotations']</filter>
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540 </data>
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diff changeset
541 </xml>
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542
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543 <xml name="annotation_orthologs_output_macro">
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diff changeset
544 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
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545 <filter>ortho_method['m'] != 'cache'</filter>
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diff changeset
546 <filter>output_options['report_orthologs']</filter>
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diff changeset
547 <actions>
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diff changeset
548 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
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549 </actions>
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550 </data>
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551 </xml>
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552
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diff changeset
553 <xml name="annotations_assertion" token_columns="21" token_add_metadata_columm_names="" token_add_column_names="" token_add_column_re="" token_nocomments="true">
12
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diff changeset
554 <output name="annotations" ftype="tabular">
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diff changeset
555 <metadata name="columns" value="@COLUMNS@" />
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556 <!-- <metadata name="column_names" value="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs@ADD_METADATA_COLUMN_NAMES@" /> -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
557 <assert_contents>
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diff changeset
558 <has_line line="#query&#009;seed_ortholog&#009;evalue&#009;score&#009;eggNOG_OGs&#009;max_annot_lvl&#009;COG_category&#009;Description&#009;Preferred_name&#009;GOs&#009;EC&#009;KEGG_ko&#009;KEGG_Pathway&#009;KEGG_Module&#009;KEGG_Reaction&#009;KEGG_rclass&#009;BRITE&#009;KEGG_TC&#009;CAZy&#009;BiGG_Reaction&#009;PFAMs@ADD_COLUMN_NAMES@"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
559 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\S+){7}\tko:\S+(\t\S+){9}@ADD_COLUMN_RE@" n="1"/>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
560 <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
561 </assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
562 </output>
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diff changeset
563 </xml>
13
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diff changeset
564 <xml name="annotations_orthologs_assertion" token_nocomments="true">
12
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diff changeset
565 <output name="annotations_orthologs" ftype="tabular">
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diff changeset
566 <metadata name="columns" value="4" />
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diff changeset
567 <metadata name="column_names" value="query,orth_type,species,orthologs" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
568 <assert_contents>
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diff changeset
569 <has_line line="#query&#009;orth_type&#009;species&#009;orthologs"/>
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diff changeset
570 <has_line_matching expression="\S+\t(one2one|many2one|one2many|many2many|seed)(\t[^\t]+){2}" n="2"/>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
571 <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
572 </assert_contents>
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diff changeset
573 </output>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
574 </xml>
13
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diff changeset
575 <token name="@HELP_ANNOTATION_OUTPUTS@"><![CDATA[
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576 **annotations**
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diff changeset
577
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
578 This file provides final annotations of each query. Tab-delimited columns in the file are:
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diff changeset
579
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580 - ``query_name``: query sequence name
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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diff changeset
581 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
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582 - ``seed_ortholog_evalue``: best protein match (e-value)
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583 - ``seed_ortholog_score``: best protein match (bit-score)
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diff changeset
584 - ``predicted_taxonomic_group``
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585 - ``predicted_protein_name``: Predicted protein name for query sequences
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diff changeset
586 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
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diff changeset
587 - ``EC_number``
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588 - ``KEGG_KO``
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589 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
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590 - ``KEGG_Module``
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591 - ``KEGG_Reaction``
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diff changeset
592 - ``KEGG_rclass``
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593 - ``BRITE``
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594 - ``KEGG_TC``
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595 - ``CAZy``
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596 - ``BiGG_Reactions``
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diff changeset
597 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
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diff changeset
598 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
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599 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
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600 - ``COG_functional_categories``: COG functional category inferred from best matching OG
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601 - ``eggNOG_free_text_description``
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602
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diff changeset
603 **orthologs**
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604
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605 This output is only created if the option ``--report_orthologs`` is checked.
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diff changeset
606 It provides the orthologs used for the annotation. It's a tab delimited file with the following columns:
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607
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608 - ``query``
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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609 - ``orth_type`` Type of orthologs in this row. See --target_orthologs.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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610 - ``species``
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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611 - ``orthologs`` comma-separated list of orthologs (If an ortholog shows a "*", such ortholog was used to transfer its annotations to the query.)
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612
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613 **sequences without annotation **
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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614
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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615 This output is created if cached annotations are used as input.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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616 It is a FASTA file containing all sequences that are not found in the cached annotations.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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617 These sequences can then be used as input for another run of the EggNOG mapper
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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618 computing seed orthologs with diamond, etc.
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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619 ]]></token>
5
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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620 </macros>