From b8c883152b8c0255aff5de3e0652e7b9d1a856cc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Dec 2024 10:41:02 +0100
Subject: [PATCH 1/3] Fix glimmer tools error handling

All the tools that call into python scripts wouldn't fail on non-zero
exit codes. They also didn't write to stderr, so in fact they could
never fail. Also fixes the remaining lint errors.
---
 tools/glimmer/.lint_skip                 |  4 ----
 tools/glimmer/glimmer_acgt_content.xml   |  4 ++--
 tools/glimmer/glimmer_build_icm.xml      |  4 ++--
 tools/glimmer/glimmer_extract.xml        |  4 ++--
 tools/glimmer/glimmer_gbk_to_orf.xml     |  8 +++----
 tools/glimmer/glimmer_glimmer_to_gff.xml |  4 ++--
 tools/glimmer/glimmer_long_orfs.xml      |  4 ++--
 tools/glimmer/glimmer_w_icm.xml          | 28 ++++++++++++++++++------
 tools/glimmer/glimmer_wo_icm.xml         | 24 ++++++++++++++------
 tools/glimmer/macros.xml                 |  1 +
 10 files changed, 53 insertions(+), 32 deletions(-)

diff --git a/tools/glimmer/.lint_skip b/tools/glimmer/.lint_skip
index 522ad865ff6..2c19ada6c9a 100644
--- a/tools/glimmer/.lint_skip
+++ b/tools/glimmer/.lint_skip
@@ -1,5 +1 @@
 CommandTODO
-InputsBoolDistinctValues
-OutputsLabelDuplicatedNoFilter
-TestsExpectNumOutputs
-XMLOrder
diff --git a/tools/glimmer/glimmer_acgt_content.xml b/tools/glimmer/glimmer_acgt_content.xml
index 593503791ad..1b5f747ca5f 100644
--- a/tools/glimmer/glimmer_acgt_content.xml
+++ b/tools/glimmer/glimmer_acgt_content.xml
@@ -1,9 +1,9 @@
-<tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@">
+<tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description>of windows in each sequence</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         window-acgt
diff --git a/tools/glimmer/glimmer_build_icm.xml b/tools/glimmer/glimmer_build_icm.xml
index fedbc84a3d8..b00735e203b 100644
--- a/tools/glimmer/glimmer_build_icm.xml
+++ b/tools/glimmer/glimmer_build_icm.xml
@@ -1,9 +1,9 @@
-<tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@">
+<tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description></description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         build-icm
diff --git a/tools/glimmer/glimmer_extract.xml b/tools/glimmer/glimmer_extract.xml
index a64953053ef..3c93acd0730 100644
--- a/tools/glimmer/glimmer_extract.xml
+++ b/tools/glimmer/glimmer_extract.xml
@@ -1,9 +1,9 @@
-<tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@">
+<tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description>from a genome</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         extract
diff --git a/tools/glimmer/glimmer_gbk_to_orf.xml b/tools/glimmer/glimmer_gbk_to_orf.xml
index 13dc40c46cf..29bc18c1baf 100644
--- a/tools/glimmer/glimmer_gbk_to_orf.xml
+++ b/tools/glimmer/glimmer_gbk_to_orf.xml
@@ -1,9 +1,9 @@
-<tool id="glimmer_gbk_to_orf" name="Extract ORF" version="@WRAPPER_VERSION@">
+<tool id="glimmer_gbk_to_orf" name="Extract ORF" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description>from a GenBank file</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         python '$__tool_directory__/glimmer_gbk_to_orf.py'
@@ -16,8 +16,8 @@
         <param name="infile" type='data' format="genbank" label="gene bank file"/>
     </inputs>
     <outputs>
-        <data name="aa_output" format="fasta" />
-        <data name="nc_output" format="fasta" />
+        <data name="aa_output" format="fasta" label="${tool.name}: Amino acids"/>
+        <data name="nc_output" format="fasta" label="{tool.name}: Nucleotides"/>
     </outputs>
     <tests>
         <test>
diff --git a/tools/glimmer/glimmer_glimmer_to_gff.xml b/tools/glimmer/glimmer_glimmer_to_gff.xml
index d82ffae9d29..18893de012c 100644
--- a/tools/glimmer/glimmer_glimmer_to_gff.xml
+++ b/tools/glimmer/glimmer_glimmer_to_gff.xml
@@ -1,9 +1,9 @@
-<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@+galaxy1">
+<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE_VERSION@">
     <description></description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         python '$__tool_directory__/glimmer_glimmer_to_gff.py'
diff --git a/tools/glimmer/glimmer_long_orfs.xml b/tools/glimmer/glimmer_long_orfs.xml
index 107cf5f6e0b..3408f19d06b 100644
--- a/tools/glimmer/glimmer_long_orfs.xml
+++ b/tools/glimmer/glimmer_long_orfs.xml
@@ -1,9 +1,9 @@
-<tool id="glimmer_long_orfs" name="Glimmer long ORFs" version="@WRAPPER_VERSION@">
+<tool id="glimmer_long_orfs" name="Glimmer long ORFs" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description>identify long, non-overlapping ORFs</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command><![CDATA[
         long-orfs
diff --git a/tools/glimmer/glimmer_w_icm.xml b/tools/glimmer/glimmer_w_icm.xml
index 32cd9feaa21..225f65de2a8 100644
--- a/tools/glimmer/glimmer_w_icm.xml
+++ b/tools/glimmer/glimmer_w_icm.xml
@@ -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**
diff --git a/tools/glimmer/glimmer_wo_icm.xml b/tools/glimmer/glimmer_wo_icm.xml
index 350ac10738f..634c6994114 100644
--- a/tools/glimmer/glimmer_wo_icm.xml
+++ b/tools/glimmer/glimmer_wo_icm.xml
@@ -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[
diff --git a/tools/glimmer/macros.xml b/tools/glimmer/macros.xml
index 420007976a9..f9a3b527603 100644
--- a/tools/glimmer/macros.xml
+++ b/tools/glimmer/macros.xml
@@ -19,4 +19,5 @@
             <citation type="doi">10.1093/bioinformatics/btm009</citation>
         </citations>
     </xml>
+    <token name="@PROFILE_VERSION@">23.1</token>
 </macros>

From 527bd084642a5c9844676b972c4a5167fbab966b Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 16 Dec 2024 14:46:05 +0100
Subject: [PATCH 2/3] Add on_string

---
 tools/glimmer/glimmer_gbk_to_orf.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/glimmer/glimmer_gbk_to_orf.xml b/tools/glimmer/glimmer_gbk_to_orf.xml
index 29bc18c1baf..d6b8bea3b9c 100644
--- a/tools/glimmer/glimmer_gbk_to_orf.xml
+++ b/tools/glimmer/glimmer_gbk_to_orf.xml
@@ -16,8 +16,8 @@
         <param name="infile" type='data' format="genbank" label="gene bank file"/>
     </inputs>
     <outputs>
-        <data name="aa_output" format="fasta" label="${tool.name}: Amino acids"/>
-        <data name="nc_output" format="fasta" label="{tool.name}: Nucleotides"/>
+        <data name="aa_output" format="fasta" label="${tool.name} on ${on_string}: Amino acids"/>
+        <data name="nc_output" format="fasta" label="{tool.name} on ${on_string}: Nucleotides"/>
     </outputs>
     <tests>
         <test>

From 2ce8adfbe80cafe8478fc6f2d0e0a78058b83e33 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Dec 2024 15:08:09 +0100
Subject: [PATCH 3/3] Bump version and use standard tokens

---
 tools/glimmer/glimmer_glimmer_to_gff.xml | 2 +-
 tools/glimmer/macros.xml                 | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/tools/glimmer/glimmer_glimmer_to_gff.xml b/tools/glimmer/glimmer_glimmer_to_gff.xml
index 18893de012c..4b2b3117516 100644
--- a/tools/glimmer/glimmer_glimmer_to_gff.xml
+++ b/tools/glimmer/glimmer_glimmer_to_gff.xml
@@ -1,4 +1,4 @@
-<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE_VERSION@">
+<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
     <description></description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/glimmer/macros.xml b/tools/glimmer/macros.xml
index f9a3b527603..dfbe640f93f 100644
--- a/tools/glimmer/macros.xml
+++ b/tools/glimmer/macros.xml
@@ -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>
@@ -12,12 +16,10 @@
             <xref type="bio.tools">gemini</xref>
         </xrefs>
     </xml>
-    <token name="@WRAPPER_VERSION@">3.02</token>
 
     <xml name="citation">
         <citations>
             <citation type="doi">10.1093/bioinformatics/btm009</citation>
         </citations>
     </xml>
-    <token name="@PROFILE_VERSION@">23.1</token>
 </macros>