Mercurial > repos > gga > genenotebook_genenotebook_build
changeset 5:bd94e502872a draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
author | gga |
---|---|
date | Tue, 24 Oct 2023 09:09:41 +0000 |
parents | ace14a8ac6e4 |
children | 12494257f0f0 |
files | genenotebook_build.xml macros.xml test-data/output/genome.tar.bz2 |
diffstat | 3 files changed, 14 insertions(+), 4 deletions(-) [+] |
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--- a/genenotebook_build.xml Tue Oct 10 15:29:02 2023 +0000 +++ b/genenotebook_build.xml Tue Oct 24 09:09:41 2023 +0000 @@ -12,7 +12,7 @@ genoboo add genome @CONNECT_INFO@ --name '${genome.name}' ${genome.public} '${genome.genome}'; #for annot in $genome.annots: - genoboo add annotation @CONNECT_INFO@ --name '${genome.name}' + genoboo add annotation @CONNECT_INFO@ --name '${genome.name}' --annot '${annot.annot}' #if $annot.prot_naming.method == 'regex' #if $annot.prot_naming.re_protein: --re_protein '$annot.prot_naming.re_protein' @@ -33,19 +33,21 @@ #else: tsv #end if + --annot '${annot.annot}' '${annot.interproscan}'; #end if #if $annot.eggnog: - genoboo add eggnog @CONNECT_INFO@ '${annot.eggnog}'; + genoboo add eggnog @CONNECT_INFO@ --annot '${annot.annot}' '${annot.eggnog}'; #end if #if $annot.hectar: - genoboo add hectar @CONNECT_INFO@ '${annot.hectar}'; + genoboo add hectar @CONNECT_INFO@ --annot '${annot.annot}' '${annot.hectar}'; #end if #if $annot.blast_cond.blast_choice == "blast": genoboo add blast @CONNECT_INFO@ + --annot '${annot.annot}' --format 'xml' --algorithm '${annot.blast_cond.algorithm}' --matrix '${annot.blast_cond.matrix}' @@ -53,6 +55,7 @@ '${annot.blast_cond.blast}'; #elif $annot.blast_cond.blast_choice == "diamond": genoboo add diamond @CONNECT_INFO@ + --annot '${annot.annot}' --format 'xml' --algorithm '${annot.blast_cond.algorithm}' --matrix '${annot.blast_cond.matrix}' @@ -62,6 +65,7 @@ #for exp in $annot.expression: genoboo add expression @CONNECT_INFO@ + --annot '${annot.annot}' --sample-description '' ${exp.public} #for replica in $exp.expression_replicas: @@ -84,6 +88,7 @@ <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" /> <repeat name="annots" title="Annotations"> <param name="annotation" label="Annotation" type="data" format="gff3" /> + <param argument="--annot" label="Annotation name" type="text" help="Annotation name" /> <conditional name="prot_naming"> <param name="method" type="select" label="Protein naming method"> <option value="none">No specific names for proteins</option> @@ -170,6 +175,7 @@ <param name="genome" value="genome.fa" /> <repeat name="annots"> <param name="annotation" value="annot.gff" /> + <param name="annot" value="My annotation" /> </repeat> </repeat> <output name="gnb_db" file="output/genome_annot.tar.bz2" compare="sim_size" /> @@ -184,6 +190,7 @@ <param name="genome" value="genome.fa" /> <repeat name="annots"> <param name="annotation" value="annot.gff" /> + <param name="annot" value="My annotation" /> <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> </repeat> </repeat> @@ -211,6 +218,7 @@ <param name="genome" value="genome.fa" /> <repeat name="annots"> <param name="annotation" value="annot.gff" /> + <param name="annot" value="My annotation" /> <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> <param name="eggnog" value="eggnog.tsv" ftype="tsv" /> <param name="hectar" value="hectar.tsv" ftype="tsv" /> @@ -230,6 +238,7 @@ <param name="genome" value="genome.fa" /> <repeat name="annots"> <param name="annotation" value="annot.gff" /> + <param name="annot" value="My annotation" /> <conditional name="prot_naming"> <param name="method" value="regex"/> @@ -265,6 +274,7 @@ <param name="genome" value="genome.fa" /> <repeat name="annots"> <param name="annotation" value="annot.gff" /> + <param name="annot" value="My annotation" /> <conditional name="prot_naming"> <param name="method" value="regex"/>
--- a/macros.xml Tue Oct 10 15:29:02 2023 +0000 +++ b/macros.xml Tue Oct 24 09:09:41 2023 +0000 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">0.4.7</token> + <token name="@TOOL_VERSION@">0.4.8</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> <xml name="citation">