| Previous changeset 2:e379c0202766 (2024-11-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4 |
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modified:
trimal.xml |
| b |
| diff -r e379c0202766 -r c2008ab22c09 trimal.xml --- a/trimal.xml Wed Nov 20 22:30:36 2024 +0000 +++ b/trimal.xml Wed Dec 03 15:44:34 2025 +0000 |
| [ |
| b'@@ -1,8 +1,9 @@\n-<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">\n+<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">\n <description>for automated alignment trimming</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.5.0</token>\n- <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@TOOL_VERSION@">1.5.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">23.0</token>\n </macros>\n <edam_topics>\n <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->\n@@ -72,11 +73,9 @@\n -soverlap\n | tee \'$statsout\'\n #end if\n-\n-\n ]]></command>\n <inputs>\n- <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />\n+ <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)"/>\n <conditional name="trimming_mode">\n <param name="mode_selector" type="select" label="Select trimming mode from the list">\n <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>\n@@ -88,7 +87,7 @@\n <option value="custom">custom mode - define trimming parameters yourself.</option>\n <option value="manual">manual mode - specify columns or sequences to remove</option>\n </param>\n- <when value="-nogaps" />\n+ <when value="-nogaps"/>\n <when value="-noallgaps"/>\n <when value="-gappyout"/>\n <when value="-strict"/>\n@@ -109,13 +108,10 @@\n <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."/>\n <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)]"/>\n <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]"/>\n-\n <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"/>\n <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)."/>\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)."/>\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)."/>\n-\n-\n </when>\n </conditional>\n <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 \xe2\x80\x9cgood position\xe2\x80\x9d. Range: [0-1]. Must be used in combination with Sequence overlap."/>\n@@ -139,94 +135,115 @@\n <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/>\n </inputs>\n <outputs>\n- <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment.">\n+ <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}:'..b'g_mode">\n+ <param name="mode_selector" value="custom"/> \n+ <param name="gapthreshold" value="0.5"/>\n+ <param name="simthreshold" value="0.5"/>\n+ <param name="conthreshold" value="0.5"/>\n+ <param name="gw" value="3"/>\n+ <param name="sw" value="4"/>\n+ <param name="cw" value="5"/>\n+ </conditional>\n <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/>\n- <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html"/>\n+ <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html" lines_diff="4"/>\n </test>\n- <test expect_num_outputs="3"><!-- test with phylip input and output statistics -->\n+ <!-- Test 05: with phylip input and output statistics -->\n+ <test expect_num_outputs="3">\n <param name="in" value="example.002.AA.phy" ftype="phylip"/>\n- <param name="mode_selector" value="-strict"/>\n+ <conditional name="trimming_mode">\n+ <param name="mode_selector" value="-strict"/>\n+ </conditional>\n <param name="statistics" value="true"/>\n- <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip" lines_diff="0"/>\n- <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="0"/>\n- <output name="statsout" file="example.002.AA.stats.txt" ftype="txt" lines_diff="0"/>\n+ <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip"/>\n+ <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="4"/>\n+ <output name="statsout" file="example.002.AA.stats.txt" ftype="txt"/>\n </test>\n- <test expect_num_outputs="2"><!-- test with overlap trimming -->\n+ <!-- Test 06: with overlap trimming -->\n+ <test expect_num_outputs="2">\n <param name="in" value="example.005.AA.fasta" ftype="fasta"/>\n- <param name="mode_selector" value="-nogaps"/>\n+ <conditional name="trimming_mode">\n+ <param name="mode_selector" value="-nogaps"/>\n+ </conditional>\n <param name="resoverlap" value="0.8"/>\n <param name="seqoverlap" value="6"/>\n- <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta" lines_diff="0"/>\n- <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="0"/>\n+ <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta"/>\n+ <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="4"/>\n </test>\n- <test expect_num_outputs="1"><!-- test with manual trimming -->\n+ <!-- Test 07: with manual trimming -->\n+ <test expect_num_outputs="1">\n <param name="in" value="example.009.AA.fasta" ftype="fasta"/>\n- <param name="mode_selector" value="manual"/>\n- <param name="selectcols" value="2,4,7-9"/>\n- <param name="selectseqs" value="1,3,5-7"/>\n- <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta" lines_diff="0"/>\n+ <conditional name="trimming_mode">\n+ <param name="mode_selector" value="manual"/>\n+ <param name="selectcols" value="2,4,7-9"/>\n+ <param name="selectseqs" value="1,3,5-7"/>\n+ </conditional>\n+ <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -259,4 +276,4 @@\n <citations>\n <citation type="doi">10.1093/bioinformatics/btp348</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |