Merge branch 'update-volcanoplot' of https://github.com/paulzierep/to…

…ols-iuc into update-volcanoplot
galaxyproject · Dec 9, 2024 · c5f616c · c5f616c
2 parents d20cf03 + 0094c93
commit c5f616c
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diff --git a/tools/ampvis2/alpha_diversity.xml b/tools/ampvis2/alpha_diversity.xml
@@ -1,4 +1,4 @@
-<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -11,13 +11,32 @@
         <configfile name="rscript"><![CDATA[
             #set m='"' + '", "'.join(str($measure).split(",")) + '"'
             library(ampvis2, quietly = TRUE)
+
             d <- readRDS("$data")
-            a <- amp_alphadiv(d,
+            table <- amp_alphadiv(d,
+                measure = c($m),
+                richness = $richness
+                @RAREFY_TOKEN@,
+            )
+            plot <- amp_alphadiv(d,
                 measure = c($m),
                 richness = $richness
-                @RAREFY_TOKEN@
+                @RAREFY_TOKEN@,
+                plot = TRUE,
+                plot_group_by = "$group_by",
+                plot_scatter = $plot_scatter
             )
-            write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE)
+            write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) 
+            ggsave("$alphadiv_plot",
+                    plot = plot,
+                    device = "$output_options.out_format"
+                    #if str($output_options.plot_width) != ''
+                        , width = $output_options.plot_width
+                    #end if
+                    #if str($output_options.plot_height) != ''
+                        , height = $output_options.plot_height
+                    #end if
+                )
         ]]></configfile>
     </configfiles>
     <inputs>
@@ -30,13 +49,19 @@
         </param>
         <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/>
         <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/>
+        <param argument="group_by" type="text" label="Group by metadata field (for plotting)" help="Specify the metadata field to group the plot by"/>
+        <param argument="plot_scatter" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scatter plot instead of boxplot?" help="Select to generate a scatter plot instead of a boxplot"/>
+        <expand macro="out_format_macro"/>
     </inputs>
     <outputs>
         <data name="alphadiv" format="tabular"/>
+        <expand macro="out_macro" name="alphadiv_plot" label=": plot"/>
     </outputs>
     <tests>
         <test>
-            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="group_by" value="Plant"/>
+            <param name="plot_scatter" value="false"/>
             <output name="alphadiv">
                 <assert_contents>
                     <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson"/>
@@ -46,12 +71,19 @@
                     <has_n_columns n="10"/>
                 </assert_contents>
             </output>
+            <output name="alphadiv_plot" ftype="pdf">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
             <param name="measure" value="observed,shannon"/> 
             <param name="richness" value="true"/>
             <param name="rarefy" value="500"/>
+            <param name="group_by" value="Plant"/>
+            <param name="plot_scatter" value="true"/>
             <output name="alphadiv">
                 <assert_contents>
                     <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson&#9;Chao1&#9;ACE"/>
@@ -62,6 +94,11 @@
                     <has_text text="&#9;500&#9;"/>
                 </assert_contents>
             </output>
+            <output name="alphadiv_plot">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/busco/busco.xml b/tools/busco/busco.xml
diff --git a/tools/busco/macros.xml b/tools/busco/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">5.7.1</token>
+    <token name="@TOOL_VERSION@">5.8.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">

diff --git a/tools/busco/test-data/genome_results/full_table b/tools/busco/test-data/genome_results/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	38486	34764	-	60.7	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94238at6656	Complete	sample	38486	34764	-	60.7	117	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing

diff --git a/tools/busco/test-data/genome_results/missing_buscos_list b/tools/busco/test-data/genome_results/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/genome_results/short_summary b/tools/busco/test-data/genome_results/short_summary
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/7/a/3/dataset_7a33f452-1064-4b4a-943f-b0efef6a4a4a.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpmwpuw5w8/files/f/d/6/dataset_fd6995c7-d1df-43b9-b8be-7e62043550f0.dat
 # BUSCO was run in mode: euk_genome_aug
 # Gene predictor used: augustus
 
@@ -24,13 +24,13 @@ Assembly Statistics:
 
 
 Dependencies and versions:
-	hmmsearch: 3.1
-	bbtools: 39.06
-	makeblastdb: 2.15.0+
-	tblastn: 2.15.0+
+	hmmsearch: 3.4
+	bbtools: None
+	makeblastdb: 2.16.0+
+	tblastn: 2.16.0+
 	augustus: 3.5.0
 	gff2gbSmallDNA.pl: None
 	new_species.pl: None
 	etraining: None
-	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
-	busco: 5.7.1
+	python: sys.version_info(major=3, minor=10, micro=14, releaselevel='final', serial=0)
+	busco: 5.8.0
diff --git a/tools/busco/test-data/genome_results_metaeuk/full_table b/tools/busco/test-data/genome_results_metaeuk/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -340,7 +340,7 @@
 68939at6656	Missing
 68961at6656	Missing
 68981at6656	Missing
-68987at6656	Complete	sample	40255	42070	+	122.8	266	https://v10-1.orthodb.org/?query=68987at6656	Nucleotidyl transferase domain
+68987at6656	Complete	sample	40255	42070	+	122.8	267	https://v10-1.orthodb.org/?query=68987at6656	Nucleotidyl transferase domain
 69201at6656	Missing
 69238at6656	Missing
 69284at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	35693	34845	-	60.6	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94238at6656	Complete	sample	35693	34845	-	60.6	117	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing

diff --git a/tools/busco/test-data/genome_results_metaeuk/missing_buscos_list b/tools/busco/test-data/genome_results_metaeuk/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/genome_results_metaeuk/summary.png b/tools/busco/test-data/genome_results_metaeuk/summary.png
diff --git a/tools/busco/test-data/genome_results_metaeuk_auto/summary.png b/tools/busco/test-data/genome_results_metaeuk_auto/summary.png
diff --git a/tools/busco/test-data/genome_results_miniprot/full_table b/tools/busco/test-data/genome_results_miniprot/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	35679	34845	-	60.7	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94238at6656	Complete	sample	35679	34845	-	60.7	117	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing

diff --git a/tools/busco/test-data/genome_results_miniprot/out.gff b/tools/busco/test-data/genome_results_miniprot/out.gff
@@ -0,0 +1,4 @@
+##gff-version 3
+sample	miniprot	mRNA	34843	35679	1341	-	.	ID=MP000459;Rank=1;Identity=0.9640;Positive=0.9856;Target=94238at6656_7220_0:000926 1 278
+sample	miniprot	CDS	34843	35679	1341	-	0	Parent=MP000459;Rank=1;Identity=0.9640;Target=94238at6656_7220_0:000926 1 278
+sample	miniprot	stop_codon	34843	34845	0	-	0	Parent=MP000459;Rank=1
diff --git a/tools/busco/test-data/proteome_results/full_table b/tools/busco/test-data/proteome_results/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	788	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
+22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	789	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing

diff --git a/tools/busco/test-data/proteome_results/missing_buscos_list b/tools/busco/test-data/proteome_results/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/proteome_results/summary.png b/tools/busco/test-data/proteome_results/summary.png
diff --git a/tools/busco/test-data/transcriptome_results/full_table b/tools/busco/test-data/transcriptome_results/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	788	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
+22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	789	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing

diff --git a/tools/busco/test-data/transcriptome_results/missing_buscos_list b/tools/busco/test-data/transcriptome_results/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/transcriptome_results/summary.png b/tools/busco/test-data/transcriptome_results/summary.png
diff --git a/tools/ensembl_vep/ensembl_vep.xml b/tools/ensembl_vep/ensembl_vep.xml
@@ -1,7 +1,7 @@
 <tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>with VEP</description>
     <macros>
-        <token name="@TOOL_VERSION@">112.0</token>
+        <token name="@TOOL_VERSION@">113.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@DB_VERSION@">108</token>
         <xml name="vcf_input">

diff --git a/tools/pretext/pretext_snapshot.xml b/tools/pretext/pretext_snapshot.xml
@@ -1,8 +1,8 @@
 <tool id="pretext_snapshot" name="Pretext Snapshot"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
         <description>image generator for Pretext contact maps</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.0.3</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">0.0.4</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pretextsnapshot</requirement>

diff --git a/tools/srst2/macros.xml b/tools/srst2/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">0.2.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="requirements">
         <requirements>

diff --git a/tools/srst2/srst2.xml b/tools/srst2/srst2.xml
@@ -103,9 +103,11 @@ srst2
 #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true
 #end if
+
 #if $use_gene_db.selector == "yes" and  $use_gene_db.no_gene_details
-&& mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutput | true
+&& mkdir -p geneTypingOutput/ geneTypingOutputFull/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutputFull | true
 #end if
+
 #if 'save_scores' in str($output_files_selector)
     && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true
 #end if
@@ -154,7 +156,7 @@ srst2
                             <add value="_" />    
                         </valid>
                     </sanitizer>
-                    <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
+                    <validator type="regex">[A-Za-z0-9 =_/+-]+</validator>
                 </param>
                 <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
                 <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
@@ -198,7 +200,11 @@ srst2
             <filter>use_mlst_db['selector'] == "yes"</filter>
         </data>  
         <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="tabular"/>
+            <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
+        </collection>         
+        <collection name="gene_typing_full" type="list" label="${tool.name} on ${on_string}: Full Gene typing results files" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutputFull" format="tabular"/>
             <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
         </collection>         
         <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results">
@@ -227,7 +233,7 @@ srst2
         </data>             
     </outputs>
     <tests>
-    <test expect_num_outputs="9">
+    <test expect_num_outputs="10">
         <param name="prob_err" value="0.01"/>
         <param name="max_unaligned_overlap" value="10"/>
         <param name="mapq" value="1"/>
@@ -264,13 +270,15 @@ srst2
             </assert_contents>
         </output>
         <output_collection name="gene_typing" type="list">
-            <element name="output__fullgenes__0-gene_db__results.txt">
+            <element name="output__genes__0-gene_db__results.txt">
                 <assert_contents>
                     <has_text text="AmpC1_Ecoli_Bla"/>
                     <has_n_lines n="2"/>
                 </assert_contents>
             </element>
-            <element name="output__genes__0-gene_db__results.txt">
+        </output_collection>
+        <output_collection name="gene_typing_full" type="list">
+            <element name="output__fullgenes__0-gene_db__results.txt">
                 <assert_contents>
                     <has_text text="AmpC1_Ecoli_Bla"/>
                     <has_n_lines n="2"/>

diff --git a/tools/ucsc_blat/blat.xml b/tools/ucsc_blat/blat.xml
@@ -1,7 +1,7 @@
 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>BLAST-like sequence alignment tool</description>
     <macros>
-        <token name="@TOOL_VERSION@">469</token>
+        <token name="@TOOL_VERSION@">472</token>
         <token name="@VERSION_SUFFIX@">0</token>
 
         <xml name="mask_cond" tokens="maskarg,label,help">

diff --git a/tools/ucsc_tools/twobittofa/twobittofa.xml b/tools/ucsc_tools/twobittofa/twobittofa.xml
@@ -1,7 +1,7 @@
 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@TOOL_VERSION@" profile="22.05">
     <description>Convert all or part of .2bit file to FASTA</description>
     <macros>
-        <token name="@TOOL_VERSION@">469</token>
+        <token name="@TOOL_VERSION@">472</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>