Mercurial > repos > galaxyp > eggnog_mapper
annotate eggnog_macros.xml @ 12:a5d5e84eed93 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
| author | galaxyp |
|---|---|
| date | Mon, 19 Jan 2026 22:22:38 +0000 |
| parents | 1f2be4ae431f |
| children |
| rev | line source |
|---|---|
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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2 <macros> |
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12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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3 <token name="@TOOL_VERSION@">2.1.13</token> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
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4 <token name="@VERSION_SUFFIX@">0</token> |
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7
9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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5 <token name="@EGGNOG_DB_VERSION@">5.0.2</token> |
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12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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6 <token name="@PROFILE@">25.0</token> |
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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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7 <!-- |
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7
9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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diff
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8 # DB versionning was super confusing for eggnog-mapper 2.0.x: |
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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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9 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) |
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7
9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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diff
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10 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0) |
|
9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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diff
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11 # (db v4.5 are not compatible with eggnog-mapper 2.0) |
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9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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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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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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13 --> |
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7
9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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14 <token name="@IDX_VERSION@">5.0.2</token> |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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15 <xml name="citations"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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16 <citations> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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17 <citation type="doi">10.1093/nar/gkv1248</citation> |
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1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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diff
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18 <citation type="doi">10.1093/molbev/msx148</citation> |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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19 </citations> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
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20 </xml> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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changeset
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21 <xml name="requirements"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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22 <requirements> |
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10
3d30526975d7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
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23 <requirement type="package" version="@TOOL_VERSION@">eggnog-mapper</requirement> |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
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24 </requirements> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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25 </xml> |
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12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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26 <xml name="biotools"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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27 <xrefs> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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28 <xref type="bio.tools">eggnog-mapper-v2</xref> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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29 </xrefs> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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30 </xml> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
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31 <xml name="version_command"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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32 <version_command>emapper.py --version</version_command> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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33 </xml> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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34 <xml name="data_manager_params"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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35 <param name="test" type="hidden" value="false" /> |
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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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36 <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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9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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37 <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."/> |
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9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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38 <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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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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39 </xml> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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40 <xml name="data_manager_outputs"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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41 <outputs> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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42 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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43 </outputs> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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44 </xml> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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45 <token name="@DOWNLOAD_CMD@"><![CDATA[ |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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46 ## tool should set install_path |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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47 #if $test == 'true' |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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48 #import os.path |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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49 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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50 #end if |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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51 mkdir -p '${install_path}' && |
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1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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52 download_eggnog_data.py |
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7
9d426cb7823b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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53 $diamond_database $mmseqs_database $pfam_database -y -q |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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54 #if $test == 'true' |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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55 -s |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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56 #end if |
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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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57 --data_dir '$install_path' && |
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1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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58 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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59 ]]></token> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
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60 <xml name="data_manager_test"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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61 <test> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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62 <param name="test" value="true"/> |
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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
5
diff
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63 <param name="diamond_database" value="true"/> |
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1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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64 <yield /> |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
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65 <output name="out_file"> |
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59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
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66 <assert_contents> |
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6
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
5
diff
changeset
|
67 <has_text text="eggnog_mapper_db_versioned" /> |
|
1d6c4af4b7bc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
5
diff
changeset
|
68 <has_text text="@EGGNOG_DB_VERSION@" /> |
|
5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
|
69 </assert_contents> |
|
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
|
70 </output> |
|
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
|
71 </test> |
|
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff
changeset
|
72 </xml> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
73 |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
74 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
75 <xml name="stdout_assertion"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
76 <assert_stdout> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
77 <has_line line="# emapper-@TOOL_VERSION@"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
78 <has_line line="FINISHED"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
79 <yield/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
80 </assert_stdout> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
81 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
82 <xml name="db_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
83 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
84 <options from_data_table="eggnog_mapper_db_versioned"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
85 <filter type="static_value" column="3" value="@IDX_VERSION@" /> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
86 </options> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
87 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
88 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
89 <token name="@DB_TOKEN@"><![CDATA[ |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
90 --data_dir '$eggnog_data.fields.path' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
91 ]]></token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
92 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
93 <!-- macros and tokens for search --> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
94 |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
95 <xml name="fasta_input"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
96 <param argument="-i" name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
97 <conditional name="input_trans"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
98 <param argument="--itype" type="select" label="Type of sequences"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
99 <option value="proteins" selected="true">proteins</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
100 <option value="CDS">CDS</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
101 <option value="genome">genome</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
102 <option value="metagenome">metagenome</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
103 </param> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
104 <when value="proteins"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
105 <when value="CDS"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
106 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
107 label="Translate CDS to proteins before search"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
108 </when> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
109 <when value="genome"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
110 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
111 label="Translate predicted CDS from blastx hits to proteins"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
112 <param argument="--genepred" type="select" label="Type of sequences"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
113 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
114 <option value="prodigal" selected="true">Performed using Prodigal</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
115 </param> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
116 </when> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
117 <when value="metagenome"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
118 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
119 label="Translate predicted CDS from blastx hits to proteins"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
120 <param argument="--genepred" type="select" label="Type of sequences"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
121 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
122 <option value="prodigal" selected="true">Performed using Prodigal</option> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
123 </param> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
124 </when> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
125 </conditional> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
126 </xml> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
127 <!-- Common options for search filtering (applies to diamond and mmseqs only) --> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
128 <xml name="common_search_options"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
129 <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" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
130 <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" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
131 <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" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
132 <param argument="--evalue" type="float" optional="true" min="0" label="Minimum query coverage" help="Report only alignments below or equal the e-value" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
133 <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" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
134 </xml> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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135 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
136 <xml name="ortho_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
137 <conditional name="ortho_method"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
138 <param argument="-m" type="select" label="Basis for annotation"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
139 <yield name="search_options"/> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
140 <yield name="reuse_options"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
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changeset
|
141 </param> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
142 <yield name="search_whens"/> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
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changeset
|
143 <yield name="reuse_whens"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
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144 </conditional> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
145 </xml> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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146 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
147 <xml name="ortho_search_macro"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
148 <expand macro="ortho_macro"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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149 <token name="search_options"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
150 <expand macro="search_options_macro"/> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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151 </token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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152 <token name="search_whens"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
153 <expand macro="search_whens_macro"/> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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154 </token> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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155 </expand> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
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156 </xml> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
157 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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158 <xml name="ortho_annotate_macro"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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159 <expand macro="ortho_macro"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
160 <token name="reuse_options"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
161 <expand macro="reuse_options_macro"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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162 </token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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163 <token name="reuse_whens"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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164 <expand macro="reuse_whens_macro"/> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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165 </token> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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166 </expand> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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167 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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168 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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169 <xml name="ortho_full_macro"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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170 <expand macro="ortho_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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171 <token name="search_options"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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172 <expand macro="search_options_macro"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
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173 </token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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174 <token name="reuse_options"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
175 <expand macro="reuse_options_macro"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
176 </token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
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177 <token name="search_whens"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
178 <expand macro="search_whens_macro"/> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
179 </token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
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180 <token name="reuse_whens"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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181 <expand macro="reuse_whens_macro"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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182 </token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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183 </expand> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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184 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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185 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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186 <xml name="search_options_macro"> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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187 <option value="diamond">Seed orthologs computed with Diamond (diamond)</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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188 <option value="mmseqs">Seed orthologs computed with MMseqs2 (mmseqs)</option> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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189 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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190 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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191 <xml name="reuse_options_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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192 <option value="no_search">Use existing seed orthologs (no_search)</option> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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193 <option value="cache">Use cached annotations (cache). See also --md5</option> |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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194 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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195 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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196 <xml name="search_whens_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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197 <when value="diamond"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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198 <expand macro="fasta_input"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
199 <conditional name="matrix_gapcosts"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
200 <param argument="--matrix" type="select" label="Scoring matrix and gap costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
201 <option value="BLOSUM90">BLOSUM90</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
202 <option value="BLOSUM80">BLOSUM80</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
203 <option value="BLOSUM62" selected="true">BLOSUM62</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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changeset
|
204 <option value="BLOSUM50">BLOSUM50</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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205 <option value="BLOSUM45">BLOSUM45</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
206 <option value="PAM250">PAM250</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
207 <option value="PAM70">PAM70</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
208 <option value="PAM30">PAM30</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
209 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
210 <when value="BLOSUM90"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
211 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
212 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
213 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
214 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
215 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
216 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
217 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
218 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
219 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
220 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
221 <when value="BLOSUM80"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
222 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
223 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
224 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
225 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
226 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
227 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
228 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
229 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
230 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
231 <when value="BLOSUM62"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
232 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
233 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
234 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
235 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
236 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
237 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
238 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
239 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
240 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
241 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
242 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
243 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
244 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
245 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
246 <when value="BLOSUM50"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
247 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
248 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
249 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
250 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
251 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
252 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
253 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
254 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
255 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
256 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
257 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
258 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
259 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
260 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
261 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
262 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
263 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
264 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
265 <when value="BLOSUM45"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
266 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
267 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
268 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
269 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
270 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
271 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
272 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
273 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
274 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
275 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
276 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
277 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
278 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
279 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
280 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
281 <when value="PAM250"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
282 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
283 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
284 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
285 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
286 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
287 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
288 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
289 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
290 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
291 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
292 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
293 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
294 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
295 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
296 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
297 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
298 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
299 <when value="PAM70"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
300 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
301 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
302 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
303 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
304 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
305 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
306 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
307 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
308 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
309 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
310 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
311 <when value="PAM30"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
312 <param name="gap_costs" type="select" label="Gap Costs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
313 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
314 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
315 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
316 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
317 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
318 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
319 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
320 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
321 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
322 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
323 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
324 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
325 </conditional> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
326 <param argument="--sensmode" type="select" label="Diamond's sensitivity mode"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
327 <option value="default">default</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
328 <option value="fast">fast</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
329 <option value="mid-sensitive">mid-sensitive</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
330 <option value="sensitive" selected="true">sensitive</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
331 <option value="more-sensitive">more-sensitive</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
332 <option value="very-sensitive">very-sensitive</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
333 <option value="ultra-sensitive">ultra-sensitive</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
334 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
335 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false" |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
336 label="Run diamond in iterative mode, up to the sensitivity level"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
337 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false" |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
338 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
339 <expand macro="common_search_options"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
340 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
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341 <when value="mmseqs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
342 <expand macro="fasta_input"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
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343 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" /> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
344 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" /> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
345 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" /> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
346 <expand macro="common_search_options"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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347 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
348 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
349 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
350 <xml name="reuse_whens_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
351 <when value="no_search"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
352 <param argument="--annotate_hits_table" type="data" multiple="true" format="tabular" label="Seed orthologs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
353 <validator type="expression" message="No seed orthologs">value.metadata.columns == 11</validator> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
354 <!-- would be cool to replace with this validator: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
355 <validator type="expression" message="No seed orthologs">value.metadata.column_names == '@SEED_ORTHOLOG_COLUMNS@'.split()</validator> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
356 but this does not work (yet) in tool tests since column_names can not be set in uploads --> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
357 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
358 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
359 <when value="cache"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
360 <expand macro="fasta_input"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
361 <param argument="--cache" type="data" format="tabular" label="EggNOG Annotations with md5 hashes" help="Annotations computed with EggNOG mapper with enabled --md5 option"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
362 <validator type="expression" message="No seed orthologs">value.metadata.columns == 22</validator> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
363 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
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364 <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."/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
365 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
366 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
367 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
368 <token name="@MERGE_ANNOTATIONS@"><![CDATA[ |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
369 #if $ortho_method.m == "no_search" |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
370 cat |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
371 #for aht in $ortho_method.annotate_hits_table |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
372 $aht |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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373 #end for |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
374 > annotate_hits_table.tsv |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
375 && |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
376 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
377 ]]></token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
378 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
379 <token name="@ORTHO_SEARCH_TOKEN@"><![CDATA[ |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
380 -m '$ortho_method.m' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
381 #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
382 -i '$ortho_method.input' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
|
383 --itype '$ortho_method.input_trans.itype' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
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384 #if $ortho_method.input_trans.itype in ['CDS', 'genome', 'metagenome']: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
385 $ortho_method.input_trans.translate |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
386 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
387 #if $ortho_method.input_trans.itype in ['genome', 'metagenome']: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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changeset
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388 --genepred $ortho_method.input_trans.genepred |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
389 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
390 #elif $ortho_method.m == "no_search" |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
391 --annotate_hits_table annotate_hits_table.tsv |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
392 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
393 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
394 #if $ortho_method.m == 'cache' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
395 --cache '$ortho_method.cache' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
396 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
397 #if $ortho_method.m == 'no_search' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
398 --annotate_hits_table annotate_hits_table.tsv |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
399 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
400 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
401 #if $ortho_method.m in ['diamond', 'mmseqs']: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
402 ## Diamond option |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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diff
changeset
|
403 #if $ortho_method.m == "diamond": |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
404 --matrix '$ortho_method.matrix_gapcosts.matrix' |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
405 $ortho_method.matrix_gapcosts.gap_costs |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
406 --sensmode $ortho_method.sensmode |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
407 $ortho_method.dmnd_iterate |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
408 $ortho_method.dmnd_ignore_warnings |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
409 #elif $ortho_method.m == "mmseqs": |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
410 --start_sens $ortho_method.start_sens |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
411 --sens_steps $ortho_method.sens_steps |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
412 --final_sens $ortho_method.final_sens |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
413 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
414 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
415 ## Common options for search filtering (applies to diamond and mmseqs only) |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
416 #if str($ortho_method.query_cover): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
417 --query_cover $ortho_method.query_cover |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
418 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
419 #if str($ortho_method.subject_cover): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
420 --subject_cover $ortho_method.subject_cover |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
421 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
422 #if str($ortho_method.pident): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
423 --pident $ortho_method.pident |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
424 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
425 #if str($ortho_method.evalue): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
426 --evalue $ortho_method.evalue |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
427 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
428 #if str($ortho_method.score): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
429 --score $ortho_method.score |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
430 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
431 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
432 ]]></token> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
433 |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
434 <!-- output options applying to search step --> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
435 <xml name="output_options_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
436 <section name="output_options" expanded="false" title="Output Options"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
437 <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true" |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
438 label="Exclude header lines and stats from output files"/> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
439 <yield/> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
440 </section> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
441 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
442 <!-- output options applying search and annotate step --> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
443 <xml name="output_options_annotate_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
444 <expand macro="output_options_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
445 <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" label="Output a file with the list of orthologs for each hit"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
446 <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false" label="Add md5 hash of each query to annotations"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
447 </expand> |
|
10
3d30526975d7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents:
7
diff
changeset
|
448 </xml> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
449 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
450 <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> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
451 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
452 <xml name="ortho_search_output_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
453 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
454 <filter>ortho_method['m'] not in ['no_search', 'cache']</filter> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
455 <actions> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
456 <action name="column_names" type="metadata" default="@SEED_ORTHOLOG_COLUMNS@"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
457 </actions> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
458 </data> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
459 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
460 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
461 <xml name="seed_orthologs_assertion" token_nocomments="true"> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
462 <output name="seed_orthologs" ftype="tabular"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
463 <assert_contents> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
464 <has_line line="#qseqid	sseqid	evalue	bitscore	qstart	qend	sstart	send	pident	qcov	scov"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
465 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\d+){4}(\t[.\d]+){3}" n="1"/> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
466 <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
467 </assert_contents> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
468 </output> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
469 </xml> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
470 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
471 <token name="@HELP_SEARCH_OUTPUTS@"><![CDATA[ |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
472 **seed orthologs** |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
473 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
474 each line in the file provides the best match of each query within the best Orthologous Group (OG) |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
475 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
476 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
477 If using the diamond search mode, seed orthologs are directly |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
478 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
479 ]]></token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
480 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
481 <!-- macros and tokens for annotate --> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
482 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
483 <xml name="annotation_options_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
484 <param argument="--seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
485 <help> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
486 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
487 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
488 </help> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
489 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
490 <param argument="--seed_ortholog_score" type="float" optional="true" min="0" label="Minimum bit score threshold"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
491 <help> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
492 Min bit score expected when searching for seed eggNOG ortholog. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
493 Queries not having a significant seed orthologs will not be annotated. |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
494 </help> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
495 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
496 <param argument="--tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" /> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
497 <param argument="--target_orthologs" type="select" label="target orthologs for functional transfer"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
498 <option value="one2one">one2one</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
499 <option value="many2one">many2one</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
500 <option value="one2many">one2many</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
501 <option value="many2many">many2many</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
502 <option value="all" selected="true">all</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
503 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
504 <param argument="--go_evidence" type="select" |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
505 label="Select the set of GO terms that should be used for annotation"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
506 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
507 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
508 <option value="all" selected="true">All (experimental + non-electronic)</option> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
509 </param> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
510 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
511 <token name="@ANNOTATION_TOKEN@"><![CDATA[ |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
512 #if str($annotation_options.seed_ortholog_evalue): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
513 --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
514 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
515 #if str($annotation_options.seed_ortholog_score): |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
516 --seed_ortholog_score $annotation_options.seed_ortholog_score |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
517 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
518 #if $annotation_options.tax_scope: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
519 --tax_scope=$annotation_options.tax_scope |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
520 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
521 #if $annotation_options.target_orthologs: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
522 --target_orthologs=$annotation_options.target_orthologs |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
523 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
524 #if $annotation_options.go_evidence: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
525 --go_evidence=$annotation_options.go_evidence |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
526 #end if |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
527 \$EGGNOG_DBMEM |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
528 ]]></token> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
529 <xml name="annotation_output_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
530 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
531 <yield/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
532 <actions> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
533 <conditional name="output_options.md5"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
534 <when value="True"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
535 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,eggNOG_OGs,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"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
536 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
537 <when value="False"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
538 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,eggNOG_OGs,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"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
539 </when> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
540 </conditional> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
541 </actions> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
542 </data> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
543 <data name="no_annotations" format="fasta" label="${tool.name} on ${on_string}: sequences without annotation" from_work_dir="results.emapper.no_annotations.fasta"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
544 <filter>ortho_method['m'] == 'cache' and ortho_method['output_no_annotations']</filter> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
545 </data> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
546 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
547 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
548 <xml name="annotation_orthologs_output_macro"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
549 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs"> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
550 <filter>ortho_method['m'] != 'cache'</filter> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
551 <filter>output_options['report_orthologs']</filter> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
552 <actions> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
553 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
554 </actions> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
555 </data> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
556 </xml> |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
557 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
558 <xml name="annotations_assertion" token_columns="21" token_add_metadata_columm_names="" token_add_column_names="" token_add_column_re="" token_nocomments="true"> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
559 <output name="annotations" ftype="tabular"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
560 <metadata name="columns" value="@COLUMNS@" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
561 <!-- <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@" /> --> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
562 <assert_contents> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
563 <has_line line="#query	seed_ortholog	evalue	score	eggNOG_OGs	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	PFAMs@ADD_COLUMN_NAMES@"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
564 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\S+){7}\tko:\S+(\t\S+){9}@ADD_COLUMN_RE@" n="1"/> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
565 <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
566 </assert_contents> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
567 </output> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
568 </xml> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
569 <xml name="annotations_orthologs_assertion" token_nocomments="true"> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
570 <output name="annotations_orthologs" ftype="tabular"> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
571 <metadata name="columns" value="4" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
572 <metadata name="column_names" value="query,orth_type,species,orthologs" /> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
573 <assert_contents> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
574 <has_line line="#query	orth_type	species	orthologs"/> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
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diff
changeset
|
575 <has_line_matching expression="\S+\t(one2one|many2one|one2many|many2many|seed)(\t[^\t]+){2}" n="2"/> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
576 <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/> |
|
11
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
577 </assert_contents> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
578 </output> |
|
1f2be4ae431f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents:
10
diff
changeset
|
579 </xml> |
|
12
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
580 <token name="@HELP_ANNOTATION_OUTPUTS@"><![CDATA[ |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
581 **annotations** |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
582 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
583 This file provides final annotations of each query. Tab-delimited columns in the file are: |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
584 |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
585 - ``query_name``: query sequence name |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
586 - ``seed_eggNOG_ortholog``: best protein match in eggNOG |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
587 - ``seed_ortholog_evalue``: best protein match (e-value) |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
588 - ``seed_ortholog_score``: best protein match (bit-score) |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
589 - ``predicted_taxonomic_group`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
590 - ``predicted_protein_name``: Predicted protein name for query sequences |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
591 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
592 - ``EC_number`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
593 - ``KEGG_KO`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
594 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
595 - ``KEGG_Module`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
596 - ``KEGG_Reaction`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
597 - ``KEGG_rclass`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
598 - ``BRITE`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
599 - ``KEGG_TC`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
600 - ``CAZy`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
601 - ``BiGG_Reactions`` |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
602 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
11
diff
changeset
|
603 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups |
|
a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
parents:
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diff
changeset
|
604 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs) |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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605 - ``COG_functional_categories``: COG functional category inferred from best matching OG |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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606 - ``eggNOG_free_text_description`` |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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607 |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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608 **orthologs** |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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609 |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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610 This output is only created if the option ``--report_orthologs`` is checked. |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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611 It provides the orthologs used for the annotation. It's a tab delimited file with the following columns: |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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612 |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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613 - ``query`` |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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614 - ``orth_type`` Type of orthologs in this row. See --target_orthologs. |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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615 - ``species`` |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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616 - ``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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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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617 |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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618 **sequences without annotation** |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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619 |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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620 This output is created if cached annotations are used as input. |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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621 It is a FASTA file containing all sequences that are not found in the cached annotations. |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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622 These sequences can then be used as input for another run of the EggNOG mapper |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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623 computing seed orthologs with diamond, etc. |
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a5d5e84eed93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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624 ]]></token> |
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5
59501122d153
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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625 </macros> |