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Update GNB to 0.4.8 #88

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Oct 24, 2023
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16 changes: 13 additions & 3 deletions tools/genenotebook/genenotebook_build.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand All @@ -33,26 +33,29 @@
#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}'
--database '${annot.blast_cond.database}'
'${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}'
Expand All @@ -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:
Expand All @@ -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>
Expand Down Expand Up @@ -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" />
Expand All @@ -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>
Expand Down Expand Up @@ -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" />
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand Down
2 changes: 1 addition & 1 deletion tools/genenotebook/macros.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down
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