changeset 7:63452ec27d36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 17b8ea9fe77df8fe1c8a2b2765b6a76ff6ebdd59-dirty

--- a/bakta.xml	Fri Jan 13 13:02:33 2023 +0000
+++ b/bakta.xml	Fri Jan 13 20:31:58 2023 +0000
@@ -12,8 +12,8 @@
 
     <command detect_errors="aggressive"><![CDATA[
         mkdir -p ./database_path/amrfinderplus-db &&
-        ln -sr '$(input_option.bakta_db_select.fields.path)'/* database_path &&
-        ln -sr '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
+        ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path &&
+        ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
         bakta
         #*======================================
                     CPU option
@@ -58,9 +58,6 @@
         #if $annotation.translation_table
             --translation-table '$annotation.translation_table'
         #end if
-        #if $annotation.gram
-            --gram '$annotation.gram'
-        #end if
         $annotation.keep_contig_headers
         #if $annotation.replicons
             --replicons '$annotation.replicons'
@@ -96,6 +93,7 @@
             </param>
             <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
                 <options from_data_table="amrfinderplus_database">
+                    <column name="value" index="0"/>
                   <validator message="No amrfinderplus database is available" type="no_options"/>
                 </options>
             </param>
@@ -126,11 +124,6 @@
                 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
                 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>
             </param>
-            <param argument="--gram" type="select" optional="true" label="Gram type for signal peptide predictions" help="Gram type +/- or unknown. Default: unknown">
-                <option value="+">Gram+</option>
-                <option value="-">Gram-</option>
-                <option value="?" selected="true">Unknown</option>
-            </param>
             <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>
             <param argument="--replicons" type="data" format="tsv,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
             <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
@@ -256,7 +249,6 @@
                <param name="plasmid" value="pOSAK1"/>
            </section>
            <section name="annotation">
-               <param name="--gram" value="-"/>
                <param name="keep_contig_headers" value="true"/>
            </section>
            <section name="workflow">
@@ -389,7 +381,7 @@
         1. You can specify if all sequences (chromosome or plasmids) are complete or not
         2. You can add your own prodigal training file for CDS predictionœ
         3. The translation table could be modified, default is the 11th for bacteria
-        4. You can specify if bacteria is gram -/+ or unknonw (default value unknow)
+        4. You can specify if bacteria is gram -/+ or unknonw (not available in galaxy tool <= 1.6.1)
         5. You can keep the name of contig present in the input file
         6. You can specify your own replicon table as a TSV/CSV file
         7. The compliance option is for ready to submit annotation file to Public database

--- a/macro.xml	Fri Jan 13 13:02:33 2023 +0000
+++ b/macro.xml	Fri Jan 13 20:31:58 2023 +0000
@@ -2,7 +2,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.6.1</token>
     <token name="@BAKTA_VERSION@">1.5</token>
-        <!--    <token name="@DEEPSIG@">1.2.5</token> -->
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
@@ -21,7 +20,6 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bakta</requirement>
-        <!--    <requirement type="package" version="@DEEPSIG@">deepsig</requirement>            -->
         </requirements>
     </xml>
     <xml name="citations">