Mercurial > repos > iuc > funannotate_annotate

changeset 8:756376aeb1ae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 1102ae206f5dfb9322d28b23d224eb67a7b80a1c
author iuc
date Wed, 01 Nov 2023 09:52:58 +0000
parents b6b5cd37f2a2
children 3bbe70fef6df
files funannotate_annotate.xml macros.xml
diffstat 2 files changed, 11 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/funannotate_annotate.xml	Fri Oct 20 10:07:28 2023 +0000
+++ b/funannotate_annotate.xml	Wed Nov 01 09:52:58 2023 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools" />
     <requirements>
         <expand macro="requirements" />
     </requirements>
@@ -66,7 +67,7 @@
 #if $remove:
     --remove '${remove}'
 #end if
-
+--header_length $header_length
 --cpus \${GALAXY_SLOTS:-2}
 
 &&
@@ -112,8 +113,6 @@
             </when>
         </conditional>
 
-
-
         <param name="database" label="Funannotate database" type="select">
             <options from_data_table="funannotate">
                 <column name="value" index="0" />
@@ -144,6 +143,7 @@
         <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID	Name	Product" />
         <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene	Product" />
 
+        <param argument="--header_length" type="integer" value="16" min="1" label="Maximum length of FASTA headers" help="The NCBI max FASTA header length is 16. Increase if you don't submit to NCBI." />
         <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
             <option value="gbk" selected="true">Annotated genome (genbank)</option>
             <option value="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option>
--- a/macros.xml	Fri Oct 20 10:07:28 2023 +0000
+++ b/macros.xml	Wed Nov 01 09:52:58 2023 +0000
@@ -1,8 +1,14 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.8.15</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-
+    <token name="@VERSION_SUFFIX@">3</token>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">
+                funannotate
+            </xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
     </xml>