Mercurial > repos > bgruening > glimmer_not_knowledge_based

changeset 3:75cedbd8cf1b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
author iuc
date Mon, 16 Dec 2024 14:42:00 +0000
parents 73c58e2debd0
children
files glimmer_wo_icm.xml macros.xml
diffstat 2 files changed, 22 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/glimmer_wo_icm.xml	Sun Mar 20 10:08:30 2022 +0000
+++ b/glimmer_wo_icm.xml	Mon Dec 16 14:42:00 2024 +0000
@@ -1,9 +1,9 @@
-<tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
+<tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         python '$__tool_directory__/glimmer_wo_icm.py'
@@ -31,20 +31,20 @@
         <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." />
         <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
 
-        <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" truevalue="" falsevalue="" 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" />
+        <param name="report" type="boolean" checked="false" label="Report the classic glimmer table output" />
     </inputs>
     <outputs>
         <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
         <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
-            <filter>report == True</filter>
+            <filter>report</filter>
         </data>
         <data name="detailed" 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="1">
             <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
             <param name="overlap" value="0" />
             <param name="gene_length" value="110" />
@@ -54,6 +54,16 @@
             <param name="report" value="" />
             <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
         </test>
+        <test expect_num_outputs="3">
+            <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
+            <param name="overlap" value="0" />
+            <param name="gene_length" value="110" />
+            <param name="threshold" value="30" />
+            <param name="linear" value="true" />
+            <param name="detailed_report" value="true" />
+            <param name="report" value="true" />
+            <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
+        </test>
     </tests>
     <help>
 <![CDATA[
--- a/macros.xml	Sun Mar 20 10:08:30 2022 +0000
+++ b/macros.xml	Mon Dec 16 14:42:00 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>