Mercurial > repos > jjohnson > eggnog_mapper
changeset 1:7de7487a7e8d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 666539d2f4b2c8f8367f1bc3786f14a45dc639f6-dirty
author | jjohnson |
---|---|
date | Tue, 08 Aug 2017 12:40:56 -0400 |
parents | b3ae16ffb54e |
children | a74d61dbd155 |
files | eggnog_mapper.xml tool-data/eggnog_mapper.loc.sample |
diffstat | 2 files changed, 40 insertions(+), 7 deletions(-) [+] |
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--- a/eggnog_mapper.xml Fri May 26 11:45:10 2017 -0400 +++ b/eggnog_mapper.xml Tue Aug 08 12:40:56 2017 -0400 @@ -29,6 +29,13 @@ #end if --Z=$db.hmm_options.Z #end if + #elif $db.mode == 'diamond': + ## $db.sensitive + ## $db.more_sensitive + --matrix '$db.matrix' + --gapopen '$db.gapopen' + --gapextend '$db.gapextend' + ## --seg '$db.seg' #end if #if $annotation_options.tax_scope: --tax_scope=$annotation_options.tax_scope @@ -69,8 +76,10 @@ <when value="hmmer"> <param name="database" type="select" multiple="true" min="1" label="HMM target database"> <options from_data_table="eggnog_mapper" > - <filter type="param_value" ref="eggnog_data" key="data_dir" column="3" /> - <filter type="static_value" name="type" value="hmm" column="2"/> + <!-- + --> + <filter type="param_value" ref="eggnog_data" column="3" /> + <filter type="static_value" name="type" value="hmmer" column="2"/> <validator type="no_options" message="No HMM DBs are available, request from your galaxy admin" /> </options> </param> @@ -92,6 +101,21 @@ </when> <when value="diamond"> <param name="database" type="hidden" value="diamond"/> + <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/> + <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/> + <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/> + <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)"> + <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option> + <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option> + <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option> + <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option> + <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option> + <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option> + <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option> + <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option> + </param> + <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" /> + <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" /> </when> </conditional> <section name="annotation_options" expanded="false" title="Annotation Options"> @@ -246,7 +270,7 @@ </actions> </data> <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations"> - <filter>output_options['no_annot'] == ''</filter> + <filter>not output_options['no_annot']</filter> <actions> <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/> </actions>
--- a/tool-data/eggnog_mapper.loc.sample Fri May 26 11:45:10 2017 -0400 +++ b/tool-data/eggnog_mapper.loc.sample Tue Aug 08 12:40:56 2017 -0400 @@ -1,9 +1,18 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of eggnog_mapper data files. # +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz +# In addition individual HMM DBs can be installed from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ +# A complete diamond database is available from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz +# +# #name value type data_dir #eggnog_4.5 eggnog_4.5 data /depot/data2/galaxy/eggnog/eggnog_4.5/data -#eggnog_4.5arcNOG arcNOG hmmer /depot/data2/galaxy/eggnog/eggnog_4.5/data -#eggnog_4.5euk euk hmmer /depot/data2/galaxy/eggnog/eggnog_4.5/data -#eggnog_4.5dmnd eggnog_proteins.dmnd diamond /depot/data2/galaxy/eggnog/eggnog_4.5/data -# +#eggnog_4.5arcNOG arcNOG hmmer eggnog_4.5 +#eggnog_4.5euk euk hmmer eggnog_4.5 +#eggnog_4.5dmnd eggnog_proteins.dmnd diamond eggnog_4.5