changeset 3:21d0af260f11 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336

--- a/glimmer_w_icm.xml	Sun Mar 20 10:06:25 2022 +0000
+++ b/glimmer_w_icm.xml	Mon Dec 16 14:42:19 2024 +0000
@@ -1,9 +1,9 @@
-<tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
+<tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description>Predict ORFs in prokaryotic genomes (knowlegde-based)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
     glimmer3
@@ -87,20 +87,20 @@
             </when>
         </conditional>
 
-        <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output"/>
-        <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file"/>
+        <param name="report" type="boolean" checked="false" label="Report the classic glimmer table output"/>
+        <param name="detailed_report" type="boolean" checked="false" label="Output a detailed gene prediction report as separate file"/>
     </inputs>
     <outputs>
         <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
         <data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
-            <filter>report == True</filter>
+            <filter>report</filter>
         </data>
         <data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
-            <filter>detailed_report == True</filter>
+            <filter>detailed_report</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
             <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
             <param name="max_olap" value="50" />
@@ -118,6 +118,20 @@
             <output name="report_output" file='glimmer_w_icm_trans-table-11_genomic.out' ftype="txt" />
             <output name="detailed_output" file='glimmer_w_icm_trans-table-11_genomic.dout' ftype="txt" lines_diff="6" />
         </test>
+        <test expect_num_outputs="1">
+            <param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
+            <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
+            <param name="max_olap" value="50" />
+            <param name="gene_len" value="90" />
+            <param name="threshold" value="30" />
+            <param name="gc_percent" value="0.0" />
+            <param name="linear" value="--linear" />
+            <param name="no_indep" value="" />
+            <param name="extend" value="" />
+            <param name="start_codons" value="atg,gtg,ttg" />
+            <param name="genbank_gencode" value="11" />
+            <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**

--- a/macros.xml	Sun Mar 20 10:06:25 2022 +0000
+++ b/macros.xml	Mon Dec 16 14:42:19 2024 +0000
@@ -1,8 +1,12 @@
 <?xml version="1.0"?>
 <macros>
+    <token name="@TOOL_VERSION@">3.02</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token>
+    <token name="@PROFILE_VERSION@">23.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.02">glimmer</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">glimmer</requirement>
             <requirement type="package" version="1.70">biopython</requirement>
             <yield/>
         </requirements>
@@ -12,7 +16,6 @@
             <xref type="bio.tools">gemini</xref>
         </xrefs>
     </xml>
-    <token name="@WRAPPER_VERSION@">3.02</token>
 
     <xml name="citation">
         <citations>