Mercurial > repos > iuc > trimal
changeset 3:c2008ab22c09 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4
| author | iuc |
|---|---|
| date | Wed, 03 Dec 2025 15:44:34 +0000 |
| parents | e379c0202766 |
| children | |
| files | trimal.xml |
| diffstat | 1 files changed, 86 insertions(+), 69 deletions(-) [+] |
line wrap: on
line diff
--- a/trimal.xml Wed Nov 20 22:30:36 2024 +0000 +++ b/trimal.xml Wed Dec 03 15:44:34 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