Mercurial > repos > pimarin > bakta

changeset 8:c75629db91ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 2479a339881bcd17ccefc0e13daab5b8f1e693af-dirty
author pimarin
date Mon, 23 Jan 2023 14:05:58 +0000
parents 63452ec27d36
children 8c7499c6f32a
files bakta.xml macro.xml test-data/amrfinderplus_database.loc
diffstat 3 files changed, 14 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/bakta.xml	Fri Jan 13 20:31:58 2023 +0000
+++ b/bakta.xml	Mon Jan 23 14:05:58 2023 +0000
@@ -58,6 +58,7 @@
         #if $annotation.translation_table
             --translation-table '$annotation.translation_table'
         #end if
+            --gram '?'
         $annotation.keep_contig_headers
         #if $annotation.replicons
             --replicons '$annotation.replicons'
@@ -93,7 +94,6 @@
             </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>
@@ -219,19 +219,18 @@
            <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>
            <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>
            <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>
-          <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
-          <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
-          <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
-          <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
-          <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
-          <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
-          <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
-          <output name="annotation_plot">
+           <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
+           <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
+           <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
+           <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
+           <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
+           <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
+           <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
+           <output name="annotation_plot">
                <assert_contents>
                    <has_size value="418991" delta="1000"/>
                </assert_contents>
            </output>
-
           <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
           <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/>
        </test>
@@ -381,7 +380,7 @@
         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 (not available in galaxy tool <= 1.6.1)
+        4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)
         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 20:31:58 2023 +0000
+++ b/macro.xml	Mon Jan 23 14:05:58 2023 +0000
@@ -1,6 +1,8 @@
 
 <macros>
     <token name="@TOOL_VERSION@">1.6.1</token>
+    <token name="@TOOL_VERSION@">1.6.1</token>
+    <token name="@TOOL_VERSION@">1.6.1</token>
     <token name="@BAKTA_VERSION@">1.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
--- a/test-data/amrfinderplus_database.loc	Fri Jan 13 20:31:58 2023 +0000
+++ b/test-data/amrfinderplus_database.loc	Mon Jan 23 14:05:58 2023 +0000
@@ -4,5 +4,5 @@
 # value, name, path
 #
 # for example
-amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2    ${__HERE__}/amrfinderplus-db/2021-09-30.1
-amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	${__HERE__}/amrfinderplus-db/2021-09-30.1
+amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2	${__HERE__}/amrfinderplus-db/latest
+amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	${__HERE__}/amrfinderplus-db/latest