Add HyPhy CLN tool wrapper

tools/hyphy/hyphy_busted.xml

@@ -245,7 +245,7 @@ BUSTED tests for positive selection by comparing a constrained model (where omeg
 MSS Methodology
 ---------------
 
-BUSTED can also incorporate models of selection on synonymous substitutions (MSS models). This is a new comparative framework for estimating selection on synonymous substitutions. These models account for selection by partitioning synonymous substitutions into multiple classes and estimating relative substitution rates for each, while also considering confounders like mutation bias. This framework allows for the study of selection on synonymous substitutions in diverse taxa without prior assumptions about the driving forces. For more information, please see the source publication: http://pubmed.ncbi.nlm.nih.gov/40129111/
+BUSTED can also incorporate models of selection on synonymous substitutions (MSS models). This is a new comparative framework for estimating selection on synonymous substitutions. These models account for selection by partitioning synonymous substitutions into multiple classes and estimating relative substitution rates for each, while also considering confounders like mutation bias. This framework allows for the study of selection on synonymous substitutions in diverse taxa without prior assumptions about the driving forces. For more information, please see the source publication: https://doi.org/10.1093/molbev/msaf068
 
 Input
 -----

tools/hyphy/hyphy_cfel.xml

@@ -79,7 +79,7 @@
             </output>
             <output name="cfel_md_report">
                 <assert_contents>
-                    <has_text text="Selected 4 branches in group _leaf_ : `Pig, Cow, Baboon, Rat`"/>
+                    <has_text text="Selected 4 branches in group _leaf_ : \`Baboon, Cow, Pig, Rat\`"/>
                     <has_text text="Permutation p-value"/>
                 </assert_contents>
             </output>

tools/hyphy/hyphy_cln.xml

@@ -0,0 +1,83 @@
+<tool id="hyphy_cln" name="HyPhy-CLN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Clean and normalize alignment</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        @SYMLINK_FILES_NO_TREE@
+        @HYPHYMP@ cln
+            --alignment input.${input_file.extension}
+            --code '$gencodeid'
+            --filtering-method '$filtering_method'
+            --output '$output_file'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,fasta.gz,nex,nexus,phylip,mega" label="Input alignment file" help="An in-frame codon alignment in one of the formats supported by HyPhy (FASTA, NEXUS, PHYLIP, or MEGA)" />
+        <expand macro="gencode"/>
+        <param argument="--filtering-method" type="select" label="Filter duplicates/gaps" help="How to filter duplicates and gaps">
+            <option value="No/No" selected="true">Keep all sequences and sites</option>
+            <option value="No/Yes">Keep all sequences, filter sites with nothing but gaps</option>
+            <option value="Yes/No">Filter duplicate sequences but keep all sites</option>
+            <option value="Yes/Yes">Filter duplicate sequences and sites with nothing but gaps</option>
+            <option value="Disallow stops">Filter duplicate sequences and all sequences that have stop codons</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: Cleaned alignment" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_file" value="conv-in1.fa"/>
+            <param name="filtering_method" value="No/No"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text=">epi_isl_1041406_hCoV_19_USA_NY_PRL_2021_02_08_05H12_2021" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_file" value="cln-stop-codons.fa"/>
+            <param name="filtering_method" value="Disallow stops"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text=">GoodSeq" />
+                    <has_text text="ATGGCGACC" />
+                    <has_text text=">StopSeq" />
+                    <has_text text="ATG---GCG" />
+                    <not_has_text text=">GoodSeqDup" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+HyPhy-CLN: Clean and Normalize Alignment
+========================================
+
+**What does this tool do?**
+
+This tool reads a sequence alignment and 'normalizes' it by cleaning sequence identifiers, removing duplicates, and/or removing gaps. It ensures the alignment is in a format suitable for other HyPhy analyses.
+
+**Options**
+
+*   **Genetic Code**: The genetic code to use for the alignment.
+*   **Filter duplicates/gaps**:
+
+    *   **Keep all sequences and sites**: No filtering is performed.
+    *   **Keep all sequences, filter sites with nothing but gaps**: Removes sites (columns) that contain only gaps.
+    *   **Filter duplicate sequences but keep all sites**: Removes duplicate sequences (identical sequences with different names or same names).
+    *   **Filter duplicate sequences and sites with nothing but gaps**: Removes both duplicate sequences and gap-only sites.
+    *   **Filter duplicate sequences and mask sequences that have stop codons**: Removes duplicates and replaces any stop codons with gaps.
+
+**Input**
+
+*   A FASTA, NEXUS, PHYLIP, or MEGA sequence alignment.
+
+**Output**
+
+*   A cleaned FASTA alignment.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>

tools/hyphy/hyphy_sm19.xml

@@ -143,7 +143,7 @@ The tool then performs permutation tests to evaluate the significance of the obs
 
 **Further reading**
 
-- https://www.ncbi.nlm.nih.gov/pubmed/2599370
+- https://doi.org/10.1093/genetics/123.3.603
 - https://github.com/veg/hyphy-analyses/tree/master/SlatkinMaddison
     ]]></help>
     <expand macro="citations">
@@ -153,7 +153,7 @@ The tool then performs permutation tests to evaluate the significance of the obs
                 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
                 year = "1989",
                 note = "Genetics 123(3):603-613",
-                url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
+                url = "https://doi.org/10.1093/genetics/123.3.603"}
         </citation>
     </expand>
 </tool>

tools/hyphy/hyphy_strike_ambigs.xml

@@ -68,10 +68,6 @@ This tool reads an alignment of coding sequences and replaces any ambiguous codo
 
 - **Ambiguous codons replaced alignment:** A FASTA format alignment where ambiguous codons have been replaced with '---'.
 - **Strike Ambigs Report:** A Markdown report summarizing the analysis, including details on how many ambiguous codons were replaced.
-
-**Further reading**
-
-- https://www.ncbi.nlm.nih.gov/pubmed/15604363
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/bioinformatics/bti079</citation>

tools/hyphy/macros.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.5.83</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.5.93</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">24.0</token>
     <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>
 

tools/hyphy/test-data/absrel-in1.fa

@@ -1,8 +1,8 @@
 >Baboon
-AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC
+AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCATCTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC
 >Cow
-------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT
+------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACTCTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT
 >Pig
----------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT
+---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGATCTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT
 >Rat
----------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC
+---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAATCTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC

tools/hyphy/test-data/annotate-out1-full.nhx

@@ -1 +1 @@
-((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated}:1e-06)Node1:1e-06,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated}:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:1e-06,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated}:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated}:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated}:0.823959)Node11{Annotated}:1e-06)Node9{Annotated}:1e-06)Node7:0.000262)Node5:1e-06)Node5
+((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated}:1e-06)Node1:1e-06,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated}:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:1e-06,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated}:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated}:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated}:0.823959)Node11{Annotated}:1e-06)Node9{Annotated}:1e-06)Node7:0.000262)Node5:1e-06)

tools/hyphy/test-data/cln-stop-codons.fa

@@ -0,0 +1,6 @@
+>GoodSeq
+ATGGCGACC
+>StopSeq
+ATGTAGGCG
+>GoodSeqDup
+ATGGCGACC

tools/hyphy/test-data/relax-in2.nex

@@ -6,7 +6,7 @@ Generated by HYPHY 0.9920070619beta(MP) for MacOS(Carbon) on Thu Jun 21 16:59:04
 ]
 
 BEGIN TAXA;
-	DIMENSIONS NTAX = 10;
+	DIMENSIONS NTAX = 4;
 	TAXLABELS
 		'Baboon' 'Cow' 'Pig' 'Rat' ;
 END;