diff trimal.xml @ 2:e379c0202766 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5

--- a/trimal.xml	Mon Nov 18 07:06:34 2024 +0000
+++ b/trimal.xml	Wed Nov 20 22:30:36 2024 +0000
@@ -1,28 +1,82 @@
-<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
     <description>for automated alignment trimming</description>
     <macros>
         <token name="@TOOL_VERSION@">1.5.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
+     <edam_topics>
+        <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->
+        <edam_topic>topic_0080</edam_topic> <!-- sequence analysis -->
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3192</edam_operation> <!--sequence trimming -->
+    </edam_operations>
     <xrefs>
         <xref type="bio.tools">trimal</xref>
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">trimal</requirement>
     </requirements>
-    <command detect_errors="exit_code"><![CDATA[    
-        trimal -in '$in' -out '$trimmed_output' -htmlout '$html_summary' ${out_format_selector}
-        #if $trimming_mode.mode_selector == "custom"
-            -gapthreshold $trimming_mode.gapthreshold
-            -simthreshold $trimming_mode.simthreshold
-            -cons $trimming_mode.cons
-        #else:
-            $trimming_mode.mode_selector
-        #end if
+    <command detect_errors="aggressive"><![CDATA[
+
+trimal -in '$in'
+-out '$trimmed_output'
+${out_format_selector}
+
+#unless $trimming_mode.mode_selector == "manual"
+  -htmlout '$html_summary'
+#end unless
+
+#if $trimming_mode.mode_selector == "custom"
+  -gapthreshold $trimming_mode.gapthreshold
+  -simthreshold $trimming_mode.simthreshold
+  -cons $trimming_mode.cons
+
+  #if $trimming_mode.w
+    -w $trimming_mode.w
+  #else
+    #if $trimming_mode.gw
+      -gw $trimming_mode.gw
+    #end if
+    #if $trimming_mode.sw
+      -sw $trimming_mode.sw
+    #end if
+    #if $trimming_mode.cw
+      -cw $trimming_mode.cw
+    #end if
+  #end if
+#else if $trimming_mode.mode_selector == "manual"
+  #if $trimming_mode.selectcols
+    -selectcols { $trimming_mode.selectcols }
+  #end if
+  #if $trimming_mode.selectseqs
+    -selectseqs { $trimming_mode.selectseqs }
+  #end if
+#else
+    $trimming_mode.mode_selector
+#end if
+
+#if $resoverlap
+  -resoverlap $resoverlap
+#end if
+#if $seqoverlap
+  -seqoverlap $seqoverlap
+#end if
+
+#if $statistics
+-sgc
+-sgt
+-ssc
+-sst
+-sident
+-soverlap
+| tee '$statsout'
+#end if
+
 
     ]]></command>
     <inputs>
-        <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" 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>
@@ -31,7 +85,8 @@
                 <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option>
                 <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option>
                 <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option>
-                <option value="custom">custom mode - eliminates a specified set of columns defined by the user.</option>
+                <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="-noallgaps"/>
@@ -39,13 +94,35 @@
             <when value="-strict"/>
             <when value="-strictplus"/>
             <when value="-automated1"/>
+            <when value="manual">
+                <param argument="-selectcols" type="text" optional="true" label="Columns to be removed from alignment" help="Example: '2,4,8-12'; Range: [0 - (Number of Columns - 1)]">
+                    <validator type="regex" message="must be comma-separated list of whole numbers">(\d+)([,-]\d+)*</validator>
+                </param>
+                <param argument="-selectseqs" type="text" optional="true" label="Sequences to be removed from alignment" help="Example: '2,4,8-12'; Range: [0 - (Number of Sequences - 1)]">
+                    <validator type="regex" message="must be comma-separated list of whole numbers">(\d+)([,-]\d+)*</validator>
+                </param>
+            </when>
             <when value="custom">
                 <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Gap threshold" help="1 - (fraction of sequences with a gap allowed)."/>
                 <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/>
+                 <param argument="-conthreshold" type="float" optional="true" min="0" max="100" label="Consistency Threshold. Minimum consistency value required" help="Range: [0 - 1]. Not allowed in combination with inputfile."/>
                 <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."/>
+        <param argument="-seqoverlap" type="integer" optional="true" min="0" max="100" label="Sequence overlap" help="Minimum percentage of “good positions” that a sequence must have in order to be conserved. Range: [0-100]. Must be used in combination with Residue overlap."/>
+
         <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
+            <option value="" selected="true">Same as input (default)</option>
             <option value="-clustal">CLUSTAL format</option>
             <option value="-fasta">FASTA format</option>
             <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option>
@@ -59,9 +136,10 @@
             <option value="-phylip3.2">PHYLIP3.2 format</option>
             <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option>
         </param>
+        <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/>
     </inputs>
     <outputs>
-        <data name="trimmed_output" format="fasta" label="Trimmed alignment.">
+        <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment.">
             <change_format>
                 <when input="out_format_selector" value="-fasta" format="fasta" />
                 <when input="out_format_selector" value="-fasta_m10" format="fasta" />
@@ -77,17 +155,22 @@
                 <when input="out_format_selector" value="-nexus" format="nexus" />
             </change_format>
         </data>
-        <data name="html_summary" format="html" label="trimal html summary."/>
+        <data name="html_summary" format="html" label="${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">
+            <filter> statistics </filter>
+        </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="2"><!-- test automated trim setting -->
             <param name="in" value="example.009.AA.fasta"/>
             <param name="mode_selector" value="-gappyout" />
             <param name="out_format_selector" value="-mega" />
-            <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/>
-            <output name="html_summary" file="trimmed_example.009.AA.html"/>
+            <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"/>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="2"><!-- test custom trim setting -->
             <param name="in" value="example.009.AA.fasta"/>
             <param name="mode_selector" value="custom" />
             <param name="gapthreshold" value="0.5" />
@@ -95,7 +178,55 @@
             <param name="cons" value="5" />
             <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"/>
+            <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/>
+        </test>
+        <test expect_num_outputs="2"><!-- test additionalcustom trim setting -->
+            <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" />
+            <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"/>
+        </test>
+         <test expect_num_outputs="2"><!-- test window settings -->
+            <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"/>
+            <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"/>
+        </test>
+        <test expect_num_outputs="3"><!-- test with phylip input and output statistics -->
+            <param name="in" value="example.002.AA.phy" ftype="phylip"/>
+            <param name="mode_selector" value="-strict"/>
+            <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"/>
+        </test>
+        <test expect_num_outputs="2"><!-- test with overlap trimming -->
+            <param name="in" value="example.005.AA.fasta" ftype="fasta"/>
+            <param name="mode_selector" value="-nogaps"/>
+            <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"/>
+        </test>
+        <test expect_num_outputs="1"><!-- test with manual trimming -->
+            <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"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -113,19 +244,19 @@
 
 - getting the complementary alignment (columns that were trimmed),
 - to compute statistics from the alignment,
-- to select the output file format, 
-- to get a summary of trimAl's trimming in HTML and SVG formats, 
+- to select the output file format,
+- to get a summary of trimAl's trimming in HTML and SVG formats,
 - and many other options.
 
-TrimAl webpage: https://trimal.readthedocs.io  
+TrimAl webpage: https://trimal.readthedocs.io
 
 License
 -------
-This program is free software: you can redistribute it and/or modify 
-it under the terms of the GNU General Public License as published by 
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
 the Free Software Foundation, the last available version.
     ]]></help>
     <citations>
-        <citation type="doi">doi:10.1093/bioinformatics/btp348</citation>
+        <citation type="doi">10.1093/bioinformatics/btp348</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>