Mercurial > repos > galaxyp > eggnog_mapper
annotate eggnog_mapper.xml @ 7:4e4c6329f6cd draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author | galaxyp |
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date | Fri, 19 Feb 2021 18:54:25 +0000 |
parents | 3cb37af59360 |
children | 96cac424c870 |
rev | line source |
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7
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
6
diff
changeset
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy1"> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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2 <description>functional sequence annotation by orthology</description> |
4
2667d24b58a0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
galaxyp
parents:
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3 <macros> |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
4
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changeset
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4 <import>eggnog_macros.xml</import> |
4
2667d24b58a0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
galaxyp
parents:
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diff
changeset
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5 </macros> |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
4
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changeset
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6 <expand macro="requirements"/> |
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
4
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changeset
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7 <expand macro="version_command"/> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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8 <command detect_errors="aggressive"><![CDATA[ |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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9 emapper.py |
5
a5a3bdd0954b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
4
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changeset
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10 --data_dir '$eggnog_data.fields.path' |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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11 -m diamond |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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12 $translate |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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changeset
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13 |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
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changeset
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14 ## Diamond option |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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15 --matrix '$diamond.matrix_gapcosts.matrix' |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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16 $diamond.matrix_gapcosts.gap_costs |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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17 --query-cover $diamond.query_cover |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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18 --subject-cover $diamond.subject_cover |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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19 |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
20 #if $annotation_options.tax_scope: |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
21 --tax_scope=$annotation_options.tax_scope |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
22 #end if |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
23 #if $annotation_options.target_orthologs: |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
24 --target_orthologs=$annotation_options.target_orthologs |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
25 #end if |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
26 #if $annotation_options.go_evidence: |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
27 --go_evidence=$annotation_options.go_evidence |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
28 #end if |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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29 #if $seed_ortholog_options.seed_ortholog_evalue: |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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30 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
31 #end if |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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32 #if str($seed_ortholog_options.seed_ortholog_score): |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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33 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
34 #end if |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
35 $output_options.no_file_comments |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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36 $output_options.no_annot |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
37 $output_options.report_orthologs |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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38 --output='results' |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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39 -i '${input}' |
1
3c7c9396daaa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9505f2a447df1bcd46ceca7b5ddb532a2f8a1cd1
galaxyp
parents:
0
diff
changeset
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40 --cpu "\${GALAXY_SLOTS:-4}" |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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41 ]]></command> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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42 <inputs> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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44 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> |
7
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
6
diff
changeset
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45 <options from_data_table="eggnog_mapper_db_versioned"> |
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
6
diff
changeset
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46 <filter type="static_value" column="3" value="@IDX_VERSION@" /> |
4e4c6329f6cd
"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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47 </options> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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48 </param> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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49 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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50 label="Are these coding DNA sequences that need to be translated?"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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51 |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
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52 <section name="diamond" expanded="true" title="Diamond Options"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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changeset
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53 <conditional name="matrix_gapcosts"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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54 <param argument="--matrix" type="select" label="Scoring matrix and gap costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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55 <option value="BLOSUM90">BLOSUM90</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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56 <option value="BLOSUM80">BLOSUM80</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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changeset
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57 <option value="BLOSUM62" selected="true">BLOSUM62</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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58 <option value="BLOSUM50">BLOSUM50</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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59 <option value="BLOSUM45">BLOSUM45</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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changeset
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60 <option value="PAM250">PAM250</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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61 <option value="PAM70">PAM70</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
62 <option value="PAM30">PAM30</option> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
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63 </param> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
64 <when value="BLOSUM90"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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65 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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66 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
67 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
68 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
69 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
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70 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
71 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
72 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
73 </param> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
74 </when> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
75 <when value="BLOSUM80"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
76 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
77 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
78 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
79 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
80 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
81 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
82 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
83 </param> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
84 </when> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
85 <when value="BLOSUM62"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
86 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
87 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
88 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
89 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
90 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
91 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
92 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
93 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
94 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
95 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
96 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
97 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
98 </param> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
99 </when> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
100 <when value="BLOSUM50"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
101 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
102 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
103 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
104 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
105 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
106 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
107 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
108 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
109 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
110 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
111 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
112 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
113 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
114 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
115 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
116 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
117 </param> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
118 </when> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
119 <when value="BLOSUM45"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
120 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
121 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
122 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
123 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
124 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
125 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
126 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
127 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
128 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
129 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
130 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
131 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
132 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
133 </param> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
134 </when> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
135 <when value="PAM250"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
136 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
137 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
138 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
139 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
140 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
141 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
142 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
143 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
144 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
145 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
146 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
147 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
148 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
149 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
150 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
151 </param> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
152 </when> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
153 <when value="PAM70"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
154 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
155 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
156 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
157 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
158 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
159 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
160 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
161 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
162 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
163 </param> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
164 </when> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
165 <when value="PAM30"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
166 <param name="gap_costs" type="select" label="Gap Costs"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
167 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
168 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
169 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
170 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
171 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
172 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
173 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
174 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
175 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
176 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
177 </param> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
178 </when> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
179 </conditional> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
180 |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
181 <param name="query_cover" type="integer" value="0" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" /> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
182 <param name="subject_cover" type="integer" value="0" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" /> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
183 </section> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
184 |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
185 <section name="annotation_options" expanded="false" title="Annotation Options"> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
changeset
|
186 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" /> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
187 <param name="target_orthologs" type="select" label="target orthologs for functional transfer"> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
188 <option value="one2one">one2one</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
189 <option value="many2one">many2one</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
190 <option value="one2many">one2many</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
191 <option value="many2many">many2many</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
192 <option value="all" selected="true">all</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
193 </param> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
194 <param name="go_evidence" type="select" |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
195 label="Select the set of GO terms that should be used for annotation"> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
196 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
197 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
198 </param> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
199 </section> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
200 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options"> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
201 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff
changeset
|
202 <help> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
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203 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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204 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated. |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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205 </help> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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206 </param> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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207 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold"> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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208 <help> |
6
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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209 Min bit score expected when searching for seed eggNOG ortholog. |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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210 Queries not having a significant seed orthologs will not be annotated. |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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211 </help> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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212 </param> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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213 </section> |
f4e5279b5d10
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214 <section name="output_options" expanded="false" title="Output Options"> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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215 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true" |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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216 label="Exclude header lines and stats from output files"/> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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217 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false" |
f4e5279b5d10
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218 label="Skip functional annotation, reporting only hits"/> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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219 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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220 label="Output a file with the list of orthologs for each hits"/> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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221 </section> |
f4e5279b5d10
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222 </inputs> |
f4e5279b5d10
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galaxyp
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223 <outputs> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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224 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs"> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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225 <actions> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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226 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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227 </actions> |
f4e5279b5d10
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228 </data> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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229 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations"> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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230 <filter>not output_options['no_annot']</filter> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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231 <actions> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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232 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_taxonomic_group,predicted_protein_name,GO_terms,EC_number,KEGG_KO,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_free_text_description"/> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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233 </actions> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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234 </data> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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235 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs"> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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236 <filter>output_options['report_orthologs']</filter> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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237 <actions> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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238 <action name="column_names" type="metadata" default="query_name,orthologs"/> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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239 </actions> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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240 </data> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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241 </outputs> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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242 <tests> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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243 <test> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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244 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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245 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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246 <param name="no_annot" value="true"/> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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247 <param name="no_file_comments" value="true"/> |
7
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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248 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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249 </test> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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250 <test> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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diff
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251 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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diff
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252 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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253 <param name="report_orthologs" value="true"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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254 <param name="no_file_comments" value="true"/> |
7
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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diff
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|
255 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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256 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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257 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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258 </test> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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259 <test> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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260 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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diff
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|
261 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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262 <param name="report_orthologs" value="true"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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diff
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|
263 <param name="no_file_comments" value="true"/> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents:
5
diff
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|
264 <section name="annotation_options"> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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265 <param name="tax_scope" value="651137" /> |
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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diff
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|
266 </section> |
7
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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diff
changeset
|
267 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
4e4c6329f6cd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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diff
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|
268 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> |
6
3cb37af59360
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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|
269 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> |
0
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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|
270 </test> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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|
271 </tests> |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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|
272 <help><![CDATA[ |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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|
273 |
f4e5279b5d10
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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274 eggnog-mapper |
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275 ============= |
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276 Overview |
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277 -------- |
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278 |
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279 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. |
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280 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. |
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281 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, |
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282 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence). |
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283 |
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284 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_. |
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285 |
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286 Outputs |
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287 ------- |
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288 |
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289 **seed_orthologs** |
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290 |
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291 each line in the file provides the best match of each query within the best Orthologous Group (OG) |
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292 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. |
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293 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. |
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294 If using the diamond search mode, seed orthologs are directly |
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295 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space. |
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296 |
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297 **annotations** |
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298 |
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299 This file provides final annotations of each query. Tab-delimited columns in the file are: |
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300 |
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301 - ``query_name``: query sequence name |
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302 - ``seed_eggNOG_ortholog``: best protein match in eggNOG |
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303 - ``seed_ortholog_evalue``: best protein match (e-value) |
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304 - ``seed_ortholog_score``: best protein match (bit-score) |
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305 - ``predicted_taxonomic_group`` |
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306 - ``predicted_protein_name``: Predicted protein name for query sequences |
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307 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms |
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308 - ``EC_number`` |
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309 - ``KEGG_KO`` |
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310 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways |
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311 - ``KEGG_Module`` |
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312 - ``KEGG_Reaction`` |
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313 - ``KEGG_rclass`` |
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314 - ``BRITE`` |
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315 - ``KEGG_TC`` |
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316 - ``CAZy`` |
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317 - ``BiGG_Reactions`` |
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318 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence |
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319 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups |
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320 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs) |
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321 - ``COG_functional_categories``: COG functional category inferred from best matching OG |
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322 - ``eggNOG_free_text_description`` |
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323 |
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324 ]]></help> |
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325 <expand macro="citations"/> |
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326 </tool> |