Mercurial > repos > gga > genenotebook_genenotebook_build

changeset 5:bd94e502872a draft

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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(-) [+]
line wrap: on
line diff
--- 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">
Binary file test-data/output/genome.tar.bz2 has changed