Merge pull request galaxyproject#6611 from pmjklemm/main

update proteinortho=6.3.4
nilchia · Dec 13, 2024 · e151cf9 · e151cf9
2 parents 8c89adc + fda6f17
commit e151cf9
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Showing 4 changed files with 74 additions and 31 deletions.
diff --git a/tools/proteinortho/proteinortho.xml b/tools/proteinortho/proteinortho.xml
@@ -99,13 +99,13 @@
             2> >(sed -E "s/.\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)
         #if $more_options.selfblast:
             &&
-            mv result.blast-graph_clean result.blast-graph;
+            mv result.blast-graph_clean result.blast-graph
         #end if
         #if $synteny.synteny_options == "specified":
             &&
             mv result.poff-graph result.proteinortho-graph &&
             mv result.poff.tsv result.proteinortho.tsv &&
-            mv result.poff.html result.proteinortho.html ;
+            mv result.poff.html result.proteinortho.html
         #end if
     ]]></command>
     <inputs>
@@ -115,6 +115,8 @@
             <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option>
             <option value="blastp">NCBI-BLASTP+ (protein sequences)</option>
             <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option>
+            <option value="mmseqsp">MMseqs2 (aminoacid sequences)</option>
+            <option value="mmseqsn">MMseqs2 (nucleotide sequences)</option>
             <option value="lastp">Last (aminoacid sequences)</option>
             <option value="lastn">Last (nucleotide sequences)</option>
             <option value="blatp">BLAT (aminoacid sequences)</option>
@@ -126,7 +128,7 @@
             <param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="Larger values results in more false positives (connections between proteins)."/>
             <param argument="--cov" type="integer" value="50" min="0" max="100" label="Minimal coverage of best blast alignments in %"/>
             <param argument="--identity" type="integer" value="25" min="0" max="100" label="Minimal percent identity of best blast hits in %"/>
-            <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs "/>
+            <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs (not compatible with synteny) "/>
             <param argument="--singles" type="boolean" checked="false" truevalue="--singles" falsevalue="" label="Report singleton genes without any hit "/>
             <param argument="--core" type="boolean" checked="false" truevalue="--core" falsevalue="" label="Stop clustering if a split would result in groups that do not span across all species of the inital connected component." help="Overrules the -conn threshold."/>
             <param argument="--isoform" type="select" label="Use isoform information" help="The reciprocal best hit graph is built using isoform information (isoforms are treated equivalent). For ncbi : simply add the additional files to the input (file names need to match). For Uniprot : the isoforms need to contain the word isoform and the corresponding identifier. For trinity simply use the trinity output format.">
@@ -137,7 +139,7 @@
             </param>
         </section>
         <conditional name="synteny">
-            <param name="synteny_options" type="select" label="Activate synteny feature (POFF)" help="To enhance the prediction accuracy, the relative order of genes (synteny) can be used as an additional feature for the discrimination of orthologs. For more details see doi:10.1371/journal.pone.0105015.">
+            <param name="synteny_options" type="select" label="Activate synteny feature (POFF)" help="To enhance the prediction accuracy, the relative order of genes (synteny) can be used as an additional feature for the discrimination of orthologs. For more details see doi:10.1371/journal.pone.0105015. (Not compatible with selfblast)">
                 <option value="no" selected="true">no</option>
                 <option value="specified">yes</option>
             </param>
@@ -177,7 +179,7 @@
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="3"> <!-- test normal -->
+        <test expect_num_outputs="3"> <!-- test normal / default params -->
             <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
             <param name="p" value="diamond"/>
             <expand macro="test_output_proteinortho" nlines="33" nlines_delta="5"/>
@@ -187,6 +189,16 @@
                 <has_text text="--p=diamond"/>
             </assert_command>
         </test>
+        <test expect_num_outputs="3"> <!-- test normal mmseqs -->
+            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
+            <param name="p" value="mmseqsp"/>
+            <expand macro="test_output_proteinortho" nlines="33" nlines_delta="5"/>
+            <expand macro="test_output_blastgraph" nlines="156" nlines_delta="20"/>
+            <expand macro="test_output_proteinorthograph" nlines="139" nlines_delta="20"/>
+            <assert_command>
+                <has_text text="--p=mmseqsp"/>
+            </assert_command>
+        </test>
         <test expect_num_outputs="3"> <!-- various parameter -->
             <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
             <param name="p" value="diamond"/>
@@ -251,12 +263,12 @@
         </test>
         <test expect_num_outputs="3"> <!-- blat -->
             <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
-            <param name="p" value="blastp"/>
+            <param name="p" value="blatp"/>
             <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>
-            <expand macro="test_output_blastgraph" nlines="156" nlines_delta="50"/>
-            <expand macro="test_output_proteinorthograph" nlines="136" nlines_delta="50"/>
+            <expand macro="test_output_blastgraph" nlines="56" nlines_delta="50"/>
+            <expand macro="test_output_proteinorthograph" nlines="56" nlines_delta="50"/>
             <assert_command>
-                <has_text text="--p=blastp"/>
+                <has_text text="--p=blatp"/>
             </assert_command>
         </test>
     </tests>
@@ -285,8 +297,8 @@ Proteinortho is a tool to detect orthologous proteins/genes within different spe
 
 * **(ii) Cluster the RBH**
 
-      | Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits.
-      | The resulting connected components are outputted in orthology-groups / -pairs 
+      | A spectral clustering algorithm is used to remove weak connections, reducing false positives.
+      | The connected components from this process are output as orthology groups or pairs.
 
 ----
 
@@ -322,41 +334,70 @@ Proteinortho is a tool to detect orthologous proteins/genes within different spe
 
       | The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups.
       | Every line corresponds to an orthology group. 
-      | The first 3 columns characterize the general properties of that group: number of proteins, species, and algebraic connectivity. The higher the algebraic connectivity the more edges are there and the better the group is connected to itself in general. 
+      | The first 3 columns characterize the general properties of that group: number of proteins, species, and algebraic connectivity. The higher the algebraic connectivity the more edges are there and the better the group is connected to itself. 
       | Then a column for each species follows containing the proteins of these species. 
       | If a species contributes with more than one protein to a group of orthologs, then they are ordered by descending connectivity.
       | The '*' represents that this species does not contribute to the group.
 
 .. csv-table::
     
-    Species,Genes,alg.-conn.,ecoli.faa,human.faa,snail.faa,wale.faa,ebola.faa
+    Species,Genes,alg.-conn.,ecoli.faa,human.faa,snail.faa,wale.faa,mouse.faa
     5,5,0.715,C_10,C_10;test,E_10,L_10,M_10
     4,6,0.115,*,C_12,E_315,L_313,M_313
     4,5,0.167,*,C_63,E_19,L_19,M_19
     4,4,0.816,*,C_64,E_18,L_18,M_18
 
+----
+
+      | The first group is comprised of 5 proteins of 5 species: 'C_10' of ecoli.faa, 'C_10;test' of human.faa, 'E_10' of snail.faa, 'L_10' of wale.faa, and 'M_10' of mouse.faa.
+      | The alg.-conn. (algebraic connectivity) of 0.715 indicates the connectivity of this group, the higher the more edges are connecting these 5 proteins (at most there can be 10 and at least there need to be 4).
+      | The second group contains 6 proteins distributed over 4 species. The star indicates the species where no protein was found (in this case ecoli.faa).
+
+.. csv-table::
+    
+    seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba    
+    # ecoli.faa,human.faa
+    # 1.91e-112,357.5,1.825e-113,360
+    L_10,C_10;test,4.32e-151,447,4.30e-151,446
+    L_11,C_11,1.17e-68,209,3.00e-69,210
+    L_14,C_14,3.64e-139,422,1.19e-142,431
+    L_15,C_15,3.51e-100,303,2.12e-102,308
+    L_16,C_16,3.75e-49,157,7.06e-50,159
+    L_17,C_17,2.96e-195,578,5.50e-196,579
+
 ----
 
 * **orthology-pairs**
 
-      | The same as orthology-groups but every edge is printed one-by-one instead of the whole group. The output is formatted the same as the RBH graph:
+      | Similar to orthology groups, but each edge is printed individually.
+      | The output is formatted the same as the RBH graph.
+      | For example extracting all hits of the second group of the example orthology-group output ('4,6,0.115,*,C_12,E_315,L_313,M_313') using grep (-E, regular expression="(C_12|E_315|L_313|M_313).*(C_12|E_315|L_313|M_313)", input file=proteinortho-graph) would reveal all edges of this groups:
 
 .. csv-table::
-    
-    seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba   
+
+    seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba    
+    M_313,C_12,1.18e-115,407,6.12e-116,407
+    C_12,E_315,4.50e-127,445,4.09e-127,445
+    L_313,M_313,0.00e+00,1368,0.00e+00,1368
+    L_313,C_12,3.76e-114,402,1.94e-114,402
 
 ----
 
+    | Especially L_313 and M_313 are very similar, probably identical.
+    | The group cotnains 4 edges out of the 6 possible edges for a group of 4 proteins. The missing edges are M_313-E_315 as well as L_313-E_315. This means that E_315 is only connected to the other 3 proteins via C_12 and thus could be considered as a weak link in the group.
+
 **Proteinortho-Tools for downstream analysis**
 
 * `proteinortho grab proteins` : find gene(s)/protein(s) in a given fasta file and retrieve their sequence(s). You can also use a orthology-groups file or a subset (e.g. filter by Species>10).
 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
 
 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
 
-**Citations:**
-
 ]]>
     </help>
-    <expand macro="citations" /> <!--- TODO: citations are not working in usegalxy, therefore they are added manually at the above. -->
+    <citations>
+        <citation type="doi">10.3389/fbinf.2023.1322477</citation>
+        <citation type="doi">10.1186/1471-2105-12-124</citation>
+        <citation type="doi">10.1371/journal.pone.0105015</citation>
+    </citations>
 </tool>
diff --git a/tools/proteinortho/proteinortho_grab_proteins.xml b/tools/proteinortho/proteinortho_grab_proteins.xml
@@ -112,5 +112,9 @@ proteinortho_grab_proteins : find gene(s)/protein(s) in a given fasta file and r
 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
 ]]>
     </help>
-    <expand macro="citations"/>
+    <citations>
+        <citation type="doi">10.3389/fbinf.2023.1322477</citation>
+        <citation type="doi">10.1186/1471-2105-12-124</citation>
+        <citation type="doi">10.1371/journal.pone.0105015</citation>
+    </citations>
 </tool>
diff --git a/tools/proteinortho/proteinortho_macros.xml b/tools/proteinortho/proteinortho_macros.xml
@@ -1,15 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@TOOL_VERSION@">6.3.1</token>
-   <token name="@WRAPPER_VERSION@">0</token>
-   <token name="@PROFILE@">22.05</token>
-   <xml name="citations">
-        <citations>
-            <citation type="doi">10.1186/1471-2105-12-124</citation>
-            <citation type="doi">10.1371/journal.pone.0105015</citation>
-            <citation type="doi">10.3389/fbinf.2023.1322477</citation>
-        </citations>
-    </xml>
+    <token name="@TOOL_VERSION@">6.3.4</token>
+    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@PROFILE@">22.05</token>
     <xml name="biotools">
         <xrefs>
             <xref type="bio.tools">proteinortho</xref>
@@ -22,6 +15,7 @@
             <requirement type="package" version="2.15.0">blast</requirement>
             <requirement type="package" version="445">ucsc-blat</requirement>
             <requirement type="package" version="1519">last</requirement>
+            <requirement type="package" version="16.747c6">mmseqs2</requirement>
         </requirements>
     </xml>
     <xml name="version_command">

diff --git a/tools/proteinortho/proteinortho_summary.xml b/tools/proteinortho/proteinortho_summary.xml
@@ -120,5 +120,9 @@ Or given 2 orthology-pairs from the same set of fasta files with different param
 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
 ]]>
     </help>
-    <expand macro="citations"/>
+    <citations>
+        <citation type="doi">10.3389/fbinf.2023.1322477</citation>
+        <citation type="doi">10.1186/1471-2105-12-124</citation>
+        <citation type="doi">10.1371/journal.pone.0105015</citation>
+    </citations>
 </tool>