Mercurial > repos > pimarin > bakta

diff bakta.xml @ 11:f93f54a21132 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit ed22b0f3b7b651e240154a08c9313585def1cfe5
author pimarin
date Mon, 13 Feb 2023 11:37:06 +0000
parents ed4bc0577be6
children
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line diff
--- a/bakta.xml	Mon Jan 23 16:41:16 2023 +0000
+++ b/bakta.xml	Mon Feb 13 11:37:06 2023 +0000
@@ -88,7 +88,7 @@
         <section name="input_option" title="Input/Output options" expanded="true">
             <param name="bakta_db_select" type="select" label="The bakta database">
                 <options from_data_table="bakta_database">
-                  <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/>
+                  <filter type="static_value" value="@BAKTA_VERSION@" column="2"/>
                   <validator message="No bakta database is available" type="no_options"/>
                 </options>
             </param>
@@ -125,7 +125,7 @@
                 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</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="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
             <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
             <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
         </section>
@@ -210,7 +210,7 @@
            <section name="input_option" >
                <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna"/>
+               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
                <param name="min_contig_length" value="250"/>
            </section>
            <section name="output_files">
@@ -238,7 +238,7 @@
            <section name="input_option" >
                <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna"/>
+               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
                <param name="min_contig_length" value="250"/>
            </section>
            <section name="organism">
@@ -274,7 +274,7 @@
            <section name="input_option" >
                <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna"/>
+               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
                <param name="min_contig_length" value="350"/>
            </section>
            <section name="workflow">
@@ -293,15 +293,15 @@
              <section name="input_option" >
                  <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                  <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-                 <param name="input_file" value="NC_002127.1.fna"/>
+                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
              </section>
              <section name="annotation">
                  <param name="complete" value="true"/>
                  <param name="prodigal" value="prodigal.tf"/>
                  <param name="translation_table" value="4"/>
-                 <param name="replicons" value="replicons.tsv"/>
+                 <param name="replicons" value="replicons.tsv" ftype="tabular"/>
                  <param name="compliant" value="true"/>
-                 <param name="proteins" value="user-proteins.faa"/>
+                 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
              </section>
              <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>
              <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
@@ -316,7 +316,7 @@
              <section name="input_option" >
                  <param name="bakta_db_select" value="V0.1_2022-08-29"/>
                  <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-                 <param name="input_file" value="NC_002127.1.fna"/>
+                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
              </section>
              <section name="annotation">
                  <param name="complete" value="true"/>