# HG changeset patch
# User iuc
# Date 1764776658 0
# Node ID 1316b4fa3c4cfa095181e9f13807c2ae60b14c3f
# Parent  46bca620b895aa45f3cab4f719f8650c6dbf2654
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4

diff -r 46bca620b895 -r 1316b4fa3c4c trimal.xml
--- a/trimal.xml	Wed Nov 20 22:30:20 2024 +0000
+++ b/trimal.xml	Wed Dec 03 15:44:18 2025 +0000
@@ -1,8 +1,9 @@
-<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
+<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description>for automated alignment trimming</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.5.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">1.5.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
     </macros>
      <edam_topics>
         <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->
@@ -72,11 +73,9 @@
 -soverlap
 | tee '$statsout'
 #end if
-
-
     ]]></command>
     <inputs>
-        <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />
+        <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)"/>
         <conditional name="trimming_mode">
             <param name="mode_selector" type="select" label="Select trimming mode from the list">
                 <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>
@@ -88,7 +87,7 @@
                 <option value="custom">custom mode - define trimming parameters yourself.</option>
                 <option value="manual">manual mode - specify columns or sequences to remove</option>
             </param>
-            <when value="-nogaps" />
+            <when value="-nogaps"/>
             <when value="-noallgaps"/>
             <when value="-gappyout"/>
             <when value="-strict"/>
@@ -109,13 +108,10 @@
                 <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/>
                 <param argument="-clusters" type="integer" optional="true" min="0" label="Clusters. Get the most Nth representatives sequences from a given alignment." help="Range:  [1 - (Number of sequences)]"/>
                 <param argument="-maxidentity" type="float" optional="true" min="0" max="1" label="Max Identity. Get the representatives sequences for a given identity threshold. " help="Range: [0 - 1]"/>
-
                 <param argument="-w" type="integer" optional="true" min="0" label="Window frame size - general" help="score of position i is the average of the window (i - n) to (i + n). Will override specific sizes set below"/>
                 <param argument="-gw" type="integer" optional="true" min="0" label="Window frame size applied to Gaps" help="score of position i is the average of the window (i - n) to (i + n)."/>
                 <param argument="-sw" type="integer" optional="true" min="0" label="Window frame size applied to Similarity" help="score of position i is the average of the window (i - n) to (i + n)."/>
                 <param argument="-cw" type="integer" optional="true" min="0" label="Window frame size applied to Consistency" help="score of position i is the average of the window (i - n) to (i + n)."/>
-
-
             </when>
         </conditional>
         <param argument="-resoverlap" type="float" optional="true" min="0" max="1" label="Residue overlap" help="Minimum overlap of a positions with other positions in the column to be considered a “good position”. Range: [0-1]. Must be used in combination with Sequence overlap."/>
@@ -139,94 +135,115 @@
         <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/>
     </inputs>
     <outputs>
-        <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment.">
+        <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment">
             <change_format>
-                <when input="out_format_selector" value="-fasta" format="fasta" />
-                <when input="out_format_selector" value="-fasta_m10" format="fasta" />
-                <when input="out_format_selector" value="-phylip" format="phylip" />
-                <when input="out_format_selector" value="-phylip_m10" format="phylip" />
-                <when input="out_format_selector" value="-phylip_paml" format="phylip" />
-                <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" />
-                <when input="out_format_selector" value="-phylip3.2" format="phylip" />
-                <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" />
-                <when input="out_format_selector" value="-clustal" format="clustal" />
-                <when input="out_format_selector" value="-mega" format="mega" />
-                <when input="out_format_selector" value="-nbrf" format="pir" />
-                <when input="out_format_selector" value="-nexus" format="nexus" />
+                <when input="out_format_selector" value="-fasta" format="fasta"/>
+                <when input="out_format_selector" value="-fasta_m10" format="fasta"/>
+                <when input="out_format_selector" value="-phylip" format="phylip"/>
+                <when input="out_format_selector" value="-phylip_m10" format="phylip"/>
+                <when input="out_format_selector" value="-phylip_paml" format="phylip"/>
+                <when input="out_format_selector" value="-phylip_paml_m10" format="phylip"/>
+                <when input="out_format_selector" value="-phylip3.2" format="phylip"/>
+                <when input="out_format_selector" value="-phylip3.2_m10" format="phylip"/>
+                <when input="out_format_selector" value="-clustal" format="clustal"/>
+                <when input="out_format_selector" value="-mega" format="mega"/>
+                <when input="out_format_selector" value="-nbrf" format="pir"/>
+                <when input="out_format_selector" value="-nexus" format="nexus"/>
             </change_format>
         </data>
         <data name="html_summary" format="html" label="${tool.name} on ${on_string}: HTML report">
             <filter> trimming_mode['mode_selector'] != 'manual' </filter>
         </data>
-        <data name="statsout" format="txt" label="${tool.name} on ${on_string}: statistics">
+        <data name="statsout" format="txt" label="${tool.name} on ${on_string}: Statistics">
             <filter> statistics </filter>
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="2"><!-- test automated trim setting -->
+        <!-- Test 01: automated trim setting -->
+        <test expect_num_outputs="2">
             <param name="in" value="example.009.AA.fasta"/>
-            <param name="mode_selector" value="-gappyout" />
-            <param name="out_format_selector" value="-mega" />
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="-gappyout"/>
+            </conditional>
+            <param name="out_format_selector" value="-mega"/>
             <output name="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/>
-            <output name="html_summary" file="trimmed_example.009.AA.html" ftype="html"/>
+            <output name="html_summary" file="trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
         </test>
-        <test expect_num_outputs="2"><!-- test custom trim setting -->
+        <!-- Test 02: custom trim setting -->
+        <test expect_num_outputs="2">
             <param name="in" value="example.009.AA.fasta"/>
-            <param name="mode_selector" value="custom" />
-            <param name="gapthreshold" value="0.5" />
-            <param name="simthreshold" value="0.5" />
-            <param name="cons" value="5" />
-            <param name="out_format_selector" value="-phylip_paml_m10" />
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="custom"/>
+                <param name="gapthreshold" value="0.5"/>
+                <param name="simthreshold" value="0.5"/>
+                <param name="cons" value="5"/>
+            </conditional>
+            <param name="out_format_selector" value="-phylip_paml_m10"/>
             <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>
-            <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/>
+            <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
         </test>
-        <test expect_num_outputs="2"><!-- test additionalcustom trim setting -->
+        <!-- Test 03: additional custom trim setting -->
+        <test expect_num_outputs="2">
             <param name="in" value="example.009.AA.fasta"/>
-            <param name="mode_selector" value="custom" />
-            <param name="gapthreshold" value="0.75" />
-            <param name="simthreshold" value="0.8" />
-            <param name="cons" value="5" />
-            <param name="conthreshold" value="0.5" />
-            <param name="clusters" value="4" />
-            <param name="maxidentity" value="0.8" />
-            <param name="out_format_selector" value="-nexus" />
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="custom"/>
+                <param name="gapthreshold" value="0.75"/>
+                <param name="simthreshold" value="0.8"/>
+                <param name="cons" value="5"/>
+                <param name="conthreshold" value="0.5"/>
+                <param name="clusters" value="4"/>
+                <param name="maxidentity" value="0.8"/>
+            </conditional>
+            <param name="out_format_selector" value="-nexus"/>
             <output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/>
-            <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/>
+            <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
         </test>
-         <test expect_num_outputs="2"><!-- test window settings -->
+        <!-- Test 04: Window settings -->
+        <test expect_num_outputs="2">
             <param name="in" value="example.005.AA.fasta"/>
-            <param name="mode_selector" value="custom" />
-            <param name="gapthreshold" value="0.5" />
-            <param name="simthreshold" value="0.5" />
-            <param name="conthreshold" value="0.5" />
-            <param name="gw" value="3"/>
-            <param name="sw" value="4"/>
-            <param name="cw" value="5"/>
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="custom"/>    
+                <param name="gapthreshold" value="0.5"/>
+                <param name="simthreshold" value="0.5"/>
+                <param name="conthreshold" value="0.5"/>
+                <param name="gw" value="3"/>
+                <param name="sw" value="4"/>
+                <param name="cw" value="5"/>
+            </conditional>
             <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/>
-            <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html"/>
+            <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html" lines_diff="4"/>
         </test>
-        <test expect_num_outputs="3"><!-- test with phylip input and output statistics -->
+        <!-- Test 05: with phylip input and output statistics -->
+        <test expect_num_outputs="3">
             <param name="in" value="example.002.AA.phy" ftype="phylip"/>
-            <param name="mode_selector" value="-strict"/>
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="-strict"/>
+            </conditional>
             <param name="statistics" value="true"/>
-            <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip" lines_diff="0"/>
-            <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="0"/>
-            <output name="statsout" file="example.002.AA.stats.txt" ftype="txt" lines_diff="0"/>
+            <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip"/>
+            <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="4"/>
+            <output name="statsout" file="example.002.AA.stats.txt" ftype="txt"/>
         </test>
-        <test expect_num_outputs="2"><!-- test with overlap trimming -->
+        <!-- Test 06: with overlap trimming -->
+        <test expect_num_outputs="2">
             <param name="in" value="example.005.AA.fasta" ftype="fasta"/>
-            <param name="mode_selector" value="-nogaps"/>
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="-nogaps"/>
+            </conditional>
             <param name="resoverlap" value="0.8"/>
             <param name="seqoverlap" value="6"/>
-            <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta" lines_diff="0"/>
-            <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="0"/>
+            <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta"/>
+            <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="4"/>
         </test>
-        <test expect_num_outputs="1"><!-- test with manual trimming -->
+        <!-- Test 07: with manual trimming -->
+        <test expect_num_outputs="1">
             <param name="in" value="example.009.AA.fasta" ftype="fasta"/>
-            <param name="mode_selector" value="manual"/>
-            <param name="selectcols" value="2,4,7-9"/>
-            <param name="selectseqs" value="1,3,5-7"/>
-            <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta" lines_diff="0"/>
+            <conditional name="trimming_mode">
+                <param name="mode_selector" value="manual"/>
+                <param name="selectcols" value="2,4,7-9"/>
+                <param name="selectseqs" value="1,3,5-7"/>
+            </conditional>
+            <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -259,4 +276,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btp348</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file