Merge pull request #6397 from B0r1sD/trimal

Add trimal
galaxyproject · Nov 15, 2024 · b537658 · b537658
2 parents fcdb311 + 8bbf4f1
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diff --git a/tools/trimal/.shed.yml b/tools/trimal/.shed.yml
@@ -0,0 +1,9 @@
+categories:
+- Phylogenetics
+description: Tool for automated alignment trimming
+homepage_url: https://trimal.readthedocs.io
+long_description: trimAl is a tool for the automated removal of spurious sequences
+  or poorly aligned regions from a multiple sequence alignment.
+name: trimal
+owner: iuc
+remote_repository_url: https://github.com/inab/trimal
diff --git a/tools/trimal/README.md b/tools/trimal/README.md
@@ -0,0 +1,3 @@
+# trimAl
+
+[trimAl](https://github.com/inab/trimal), a tool for automated alignment trimming in large-scale phylogenetic analyses.
diff --git a/tools/trimal/test-data/custom_trimmed_example.009.AA.html b/tools/trimal/test-data/custom_trimmed_example.009.AA.html
diff --git a/tools/trimal/test-data/custom_trimmed_example.009.AA.phy b/tools/trimal/test-data/custom_trimmed_example.009.AA.phy
@@ -0,0 +1,11 @@
+ 9 63
+Csa004271    --------------YMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Xtr21234     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaH         SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Hsa167996    SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Mmu024661    SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Dre37936     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaM         SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Tru14292     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Ola20972     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+
diff --git a/tools/trimal/test-data/example.004.AA.fasta b/tools/trimal/test-data/example.004.AA.fasta
@@ -0,0 +1,18 @@
+>Sp8
+FPWNGLQIHMMGIII
+
+>Sp17
+FPWNGLQIHMMGIII
+
+>Sp10
+FPWNGLQIHMMGIII
+
+>Sp26
+FPWNGLQIHMMGIII
+
+>Sp33
+FPWNGLQIHMMGIII
+
+>Sp6
+FPWNGLQIHMMGIII
+
diff --git a/tools/trimal/test-data/example.009.AA.fasta b/tools/trimal/test-data/example.009.AA.fasta
@@ -0,0 +1,45 @@
+>Csa004271
+---------------------------------MYMAMGHFFDRDDVALKNISEYFKECS
+EEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL
+HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS
+-----
+>Xtr21234
+----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQS
+KEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL
+HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS-
+-----
+>LcaH
+----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQS
+HEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL
+HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGK
+ES--S
+>Hsa167996
+MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL
+HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGD
+SDNES
+>Mmu024661
+MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL
+HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGH
+GD-ES
+>Dre37936
+---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNS
+EEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL
+HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS
+-----
+>LcaM
+----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENS
+DEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL
+HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGG
+KS---
+>Tru14292
+----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENS
+DEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL
+HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGS
+KS---
+>Ola20972  	
+----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENS
+HEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL
+HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGS
+KS---
diff --git a/tools/trimal/test-data/trimmed_example.009.AA.html b/tools/trimal/test-data/trimmed_example.009.AA.html
diff --git a/tools/trimal/test-data/trimmed_example.009.AA.mega b/tools/trimal/test-data/trimmed_example.009.AA.mega
@@ -0,0 +1,58 @@
+#MEGA
+!Title ./test-data/example.009.AA.fasta;
+!Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard;
+
+#Csa004271
+---------- ---------- ---------M YMAMGHFFDR DDVALKNISE 
+YFKECSEEER EHANKMIEFH NKRGGTTTYF PIKAPGSFDP ANTIKAMNCA 
+LALEVNVNKS LLALHE--TA NGDPEFQDFI EANFLHEQVD AIKKLKDYIT 
+NLKLVG---T GLGEFLFDKH FKSS 
+
+#Xtr21234
+MISQVRQNYS HDCEAAVNRM VNLEMYASYT YLSMSHYFDR DDVALHHVAE 
+FFKEQSKEER ECAEKLMKCQ NKRGGRIVLQ DIKKPERDEW GSTLDAMQTA 
+LDLEKHVNQA LLDLHNLATE RKDPHICDFL ESEHLDEQVK HMKKFGDHIT 
+NLKRLGVPQN GMGEYLFDKH SLS- 
+
+#LcaH
+MSSQVRQNFH QDCEAAINRQ INLELYASYV YLSMAYYFDR DDQALHNFAK 
+FFRHQSHEER EHAEKLMKLQ NQRGGRIFLQ DVRKPDRDEW GSGVEALECA 
+LQLEKSVNQS LLDLHKLCSD HNDPHLCDFI ETHYLDEQVK SIKELADWVT 
+NLRRMGAPQN GMAEYLFDKH TLGK 
+
+#Hsa167996
+STSQVRQNYH QDSEAAINRQ INLELYASYV YLSMSYYFDR DDVALKNFAK 
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDCDDW ESGLNAMECA 
+LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT 
+NLRKMGAPES GLAEYLFDKH TLGD 
+
+#Mmu024661
+SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK 
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDDW ESGLNAMECA 
+LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT 
+NLRKMGAPEA GMAEYLFDKH TLGH 
+
+#Dre37936
+ETSQIRQNYV RDCEAAINKM INLELYAGYT YTSMAHYFKR DDVALPGFAK 
+FFKKNSEEER EHAEKFMEFQ NKRGGRIVLQ DIKKPDRDVW GNGLIAMQCA 
+LQLEKNVNQA LLDLHKLATE MGDPHLCDFL ETHYLNEQVE AIKKLGDHIT 
+NLSKMDAGNN RMAEYLFDKH TLDS 
+
+#LcaM
+MESQVRQNYH RDCEAAVNRM VNMEMFASYT YTSMAFYFSR DDVALPGFSH 
+FFKENSDEER EHAEKLLSFQ NKRGGHIFLQ DIKKPERDEW GSGLEAMQCA 
+LQLKKNVNQA LLDLHKLASD HGDPHLCDFL ETHYLNEQVE AIKKLGDYIS 
+NLSRMDAQKN KMAEYLFDKH SLGG 
+
+#Tru14292
+MESQVRQNYH RDCEAAINKM INMELYASYT YTSMAFFFSR DDVALPGFAH 
+FFKENSDEER EHAEKLLSFQ NKRGGRIFLQ DIKKPERDEW GSGLEAMQCA 
+LQLEKKVNQA LLDLHKLASD HVDPHLCDFL ESHYLNEQVE AIKKLGDYIT 
+NLSRMDAQNN KMAEYLFDKH TLGS 
+
+#Ola20972
+MESQVRQNYH RDCEAAINRM VNMELFASYT YTSMAFYFDR DDVALPGFSH 
+FFKENSHEEK EHADKLLSFQ NKRGGRIFLQ DVKKPERDEW GSGLEAMQCA 
+LQLEKNVNQA LLDLHKVASD HKDPHMCDFL ETHYLNEQVE SIKKIGDHIT 
+NLTRMDAHTN KMAEYLFDKH TLGS 
+
diff --git a/tools/trimal/trimal.xml b/tools/trimal/trimal.xml
@@ -0,0 +1,131 @@
+<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+    <description>for automated alignment trimming</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.5</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <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>
+    <inputs>
+        <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" 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>
+            </param>
+            <when value="-nogaps" />
+            <when value="-noallgaps"/>
+            <when value="-gappyout"/>
+            <when value="-strict"/>
+            <when value="-strictplus"/>
+            <when value="-automated1"/>
+            <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="-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."/>
+            </when>
+        </conditional>
+        <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
+            <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="-mega">MEGA format</option>
+            <option value="-phylip">PHYLIP/PHYLIP4 format</option>
+            <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</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>
+    </inputs>
+    <outputs>
+        <data name="trimmed_output" format="fasta" label="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" />
+            </change_format>
+        </data>
+        <data name="html_summary" format="html" label="trimal html summary."/>
+    </outputs>
+    <tests>
+        <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" />
+            <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/>
+            <output name="html_summary" file="trimmed_example.009.AA.html"/>
+        </test>
+        <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" />
+            <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>
+            <output name="html_summary" file="custom_trimmed_example.009.AA.html"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
+
+TrimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment.
+These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided,
+the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment.
+
+TrimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics
+of the input alignment, to be used so that the signal-to-noise ratio after alignment trimming phase is increased. Learn more about the available trimming modes here: https://trimal.readthedocs.io/en/latest/algorithms.html
+
+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>
+    </citations>
+</tool>