trimal: trimal.xml comparison

comparison trimal.xml @ 2:e379c0202766 draft default tip

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

author	iuc
date	Wed, 20 Nov 2024 22:30:36 +0000
parents	2a156ec81e7a
children

comparison

equal deleted inserted replaced

-:2a156ec81e7a
+:e379c0202766
-<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[
+<command detect_errors="aggressive"><![CDATA[
-trimal -in '$in' -out '$trimmed_output' -htmlout '$html_summary' ${out_format_selector}
-#if $trimming_mode.mode_selector == "custom"
+trimal -in '$in'
--gapthreshold $trimming_mode.gapthreshold
+-out '$trimmed_output'
--simthreshold $trimming_mode.simthreshold
+${out_format_selector}
--cons $trimming_mode.cons
-#else:
+#unless $trimming_mode.mode_selector == "manual"
-$trimming_mode.mode_selector
+-htmlout '$html_summary'
-#end if
+#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>
 <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option>
 <option value="-gappyout">gappyout - only uses information based on gaps' distribution.</option>
 <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"/>
 <when value="-gappyout"/>
 <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>
 <option value="-nbrf">NBRF/PIR format</option>
 <option value="-nexus">NEXUS format</option>
 <option value="-phylip_paml">PHYLIP format compatible with PAML</option>
 <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option>
 <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 ${on_string}: Trimmed alignment.">
 <change_format>
 <when input="out_format_selector" value="-fasta" format="fasta" />
 <when input="out_format_selector" value="-fasta_m10" format="fasta" />
 <when input="out_format_selector" value="-phylip" format="phylip" />
 <when input="out_format_selector" value="-phylip_m10" format="phylip" />
 <when input="out_format_selector" value="-mega" format="mega" />
 <when input="out_format_selector" value="-nbrf" format="pir" />
 <when input="out_format_selector" value="-nexus" format="nexus" />
 </change_format>
 </data>
-<data name="html_summary" format="html" label="trimal html summary."/>
+<data name="html_summary" format="html" label="${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="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/>
-<output name="html_summary" file="trimmed_example.009.AA.html"/>
+<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" />
 <param name="simthreshold" value="0.5" />
 <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[
 TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
 Among trimAl's additional features, trimAl allows:
 - 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,
 - and many other options.
 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
 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>

Mercurial > repos > iuc > trimal

comparison trimal.xml @ 2:e379c0202766 draft default tip