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Merge pull request #7505 from SaimMomin12/tools/trimal
Update and Fix tools/trimal
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‎tools/trimal/.lint_skip‎

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‎tools/trimal/trimal.xml‎

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<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
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<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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<description>for automated alignment trimming</description>
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<macros>
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<token name="@TOOL_VERSION@">1.5.0</token>
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<token name="@VERSION_SUFFIX@">1</token>
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<token name="@TOOL_VERSION@">1.5.1</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@PROFILE@">23.0</token>
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</macros>
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<edam_topics>
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<edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->
@@ -72,11 +73,9 @@ ${out_format_selector}
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-soverlap
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| tee '$statsout'
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#end if
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]]></command>
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<inputs>
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<param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />
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<param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)"/>
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<conditional name="trimming_mode">
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<param name="mode_selector" type="select" label="Select trimming mode from the list">
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<option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>
@@ -88,7 +87,7 @@ ${out_format_selector}
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<option value="custom">custom mode - define trimming parameters yourself.</option>
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<option value="manual">manual mode - specify columns or sequences to remove</option>
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</param>
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<when value="-nogaps" />
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<when value="-nogaps"/>
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<when value="-noallgaps"/>
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<when value="-gappyout"/>
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<when value="-strict"/>
@@ -109,13 +108,10 @@ ${out_format_selector}
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<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."/>
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<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)]"/>
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<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]"/>
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<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"/>
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<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)."/>
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<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)."/>
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<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)."/>
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</when>
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</conditional>
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<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 @@ ${out_format_selector}
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<param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/>
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</inputs>
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<outputs>
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<data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment.">
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<data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment">
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<change_format>
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<when input="out_format_selector" value="-fasta" format="fasta" />
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<when input="out_format_selector" value="-fasta_m10" format="fasta" />
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<when input="out_format_selector" value="-phylip" format="phylip" />
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<when input="out_format_selector" value="-phylip_m10" format="phylip" />
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<when input="out_format_selector" value="-phylip_paml" format="phylip" />
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<when input="out_format_selector" value="-phylip_paml_m10" format="phylip" />
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<when input="out_format_selector" value="-phylip3.2" format="phylip" />
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<when input="out_format_selector" value="-phylip3.2_m10" format="phylip" />
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<when input="out_format_selector" value="-clustal" format="clustal" />
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<when input="out_format_selector" value="-mega" format="mega" />
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<when input="out_format_selector" value="-nbrf" format="pir" />
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<when input="out_format_selector" value="-nexus" format="nexus" />
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<when input="out_format_selector" value="-fasta" format="fasta"/>
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<when input="out_format_selector" value="-fasta_m10" format="fasta"/>
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<when input="out_format_selector" value="-phylip" format="phylip"/>
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<when input="out_format_selector" value="-phylip_m10" format="phylip"/>
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<when input="out_format_selector" value="-phylip_paml" format="phylip"/>
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<when input="out_format_selector" value="-phylip_paml_m10" format="phylip"/>
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<when input="out_format_selector" value="-phylip3.2" format="phylip"/>
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<when input="out_format_selector" value="-phylip3.2_m10" format="phylip"/>
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<when input="out_format_selector" value="-clustal" format="clustal"/>
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<when input="out_format_selector" value="-mega" format="mega"/>
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<when input="out_format_selector" value="-nbrf" format="pir"/>
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<when input="out_format_selector" value="-nexus" format="nexus"/>
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</change_format>
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</data>
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<data name="html_summary" format="html" label="${tool.name} on ${on_string}: HTML report">
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<filter> trimming_mode['mode_selector'] != 'manual' </filter>
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</data>
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<data name="statsout" format="txt" label="${tool.name} on ${on_string}: statistics">
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<data name="statsout" format="txt" label="${tool.name} on ${on_string}: Statistics">
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<filter> statistics </filter>
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</data>
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</outputs>
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<tests>
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<test expect_num_outputs="2"><!-- test automated trim setting -->
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<!-- Test 01: automated trim setting -->
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<test expect_num_outputs="2">
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<param name="in" value="example.009.AA.fasta"/>
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<param name="mode_selector" value="-gappyout" />
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<param name="out_format_selector" value="-mega" />
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<conditional name="trimming_mode">
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<param name="mode_selector" value="-gappyout"/>
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</conditional>
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<param name="out_format_selector" value="-mega"/>
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<output name="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/>
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<output name="html_summary" file="trimmed_example.009.AA.html" ftype="html"/>
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<output name="html_summary" file="trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
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</test>
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<test expect_num_outputs="2"><!-- test custom trim setting -->
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<!-- Test 02: custom trim setting -->
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<test expect_num_outputs="2">
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<param name="in" value="example.009.AA.fasta"/>
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<param name="mode_selector" value="custom" />
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<param name="gapthreshold" value="0.5" />
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<param name="simthreshold" value="0.5" />
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<param name="cons" value="5" />
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<param name="out_format_selector" value="-phylip_paml_m10" />
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<conditional name="trimming_mode">
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<param name="mode_selector" value="custom"/>
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<param name="gapthreshold" value="0.5"/>
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<param name="simthreshold" value="0.5"/>
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<param name="cons" value="5"/>
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</conditional>
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<param name="out_format_selector" value="-phylip_paml_m10"/>
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<output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>
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<output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/>
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<output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
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</test>
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<test expect_num_outputs="2"><!-- test additionalcustom trim setting -->
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<!-- Test 03: additional custom trim setting -->
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<test expect_num_outputs="2">
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<param name="in" value="example.009.AA.fasta"/>
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<param name="mode_selector" value="custom" />
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<param name="gapthreshold" value="0.75" />
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<param name="simthreshold" value="0.8" />
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<param name="cons" value="5" />
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<param name="conthreshold" value="0.5" />
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<param name="clusters" value="4" />
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<param name="maxidentity" value="0.8" />
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<param name="out_format_selector" value="-nexus" />
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<conditional name="trimming_mode">
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<param name="mode_selector" value="custom"/>
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<param name="gapthreshold" value="0.75"/>
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<param name="simthreshold" value="0.8"/>
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<param name="cons" value="5"/>
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<param name="conthreshold" value="0.5"/>
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<param name="clusters" value="4"/>
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<param name="maxidentity" value="0.8"/>
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</conditional>
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<param name="out_format_selector" value="-nexus"/>
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<output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/>
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<output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/>
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<output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
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</test>
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<test expect_num_outputs="2"><!-- test window settings -->
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<!-- Test 04: Window settings -->
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<test expect_num_outputs="2">
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<param name="in" value="example.005.AA.fasta"/>
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<param name="mode_selector" value="custom" />
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<param name="gapthreshold" value="0.5" />
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<param name="simthreshold" value="0.5" />
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<param name="conthreshold" value="0.5" />
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<param name="gw" value="3"/>
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<param name="sw" value="4"/>
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<param name="cw" value="5"/>
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<conditional name="trimming_mode">
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<param name="mode_selector" value="custom"/>
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<param name="gapthreshold" value="0.5"/>
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<param name="simthreshold" value="0.5"/>
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<param name="conthreshold" value="0.5"/>
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<param name="gw" value="3"/>
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<param name="sw" value="4"/>
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<param name="cw" value="5"/>
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</conditional>
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<output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/>
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<output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html"/>
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<output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html" lines_diff="4"/>
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</test>
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<test expect_num_outputs="3"><!-- test with phylip input and output statistics -->
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<!-- Test 05: with phylip input and output statistics -->
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<test expect_num_outputs="3">
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<param name="in" value="example.002.AA.phy" ftype="phylip"/>
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<param name="mode_selector" value="-strict"/>
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<conditional name="trimming_mode">
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<param name="mode_selector" value="-strict"/>
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</conditional>
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<param name="statistics" value="true"/>
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<output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip" lines_diff="0"/>
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<output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="0"/>
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<output name="statsout" file="example.002.AA.stats.txt" ftype="txt" lines_diff="0"/>
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<output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip"/>
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<output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="4"/>
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<output name="statsout" file="example.002.AA.stats.txt" ftype="txt"/>
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</test>
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<test expect_num_outputs="2"><!-- test with overlap trimming -->
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<!-- Test 06: with overlap trimming -->
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<test expect_num_outputs="2">
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<param name="in" value="example.005.AA.fasta" ftype="fasta"/>
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<param name="mode_selector" value="-nogaps"/>
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<conditional name="trimming_mode">
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<param name="mode_selector" value="-nogaps"/>
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</conditional>
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<param name="resoverlap" value="0.8"/>
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<param name="seqoverlap" value="6"/>
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<output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta" lines_diff="0"/>
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<output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="0"/>
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<output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta"/>
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<output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="4"/>
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</test>
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<test expect_num_outputs="1"><!-- test with manual trimming -->
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<!-- Test 07: with manual trimming -->
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<test expect_num_outputs="1">
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<param name="in" value="example.009.AA.fasta" ftype="fasta"/>
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<param name="mode_selector" value="manual"/>
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<param name="selectcols" value="2,4,7-9"/>
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<param name="selectseqs" value="1,3,5-7"/>
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<output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta" lines_diff="0"/>
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<conditional name="trimming_mode">
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<param name="mode_selector" value="manual"/>
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<param name="selectcols" value="2,4,7-9"/>
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<param name="selectseqs" value="1,3,5-7"/>
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</conditional>
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<output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta"/>
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</test>
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</tests>
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<help><![CDATA[
@@ -259,4 +276,4 @@ the Free Software Foundation, the last available version.
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<citations>
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<citation type="doi">10.1093/bioinformatics/btp348</citation>
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</citations>
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</tool>
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</tool>

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