# HG changeset patch
# User iuc
# Date 1724753627 0
# Node ID ed2c532794c1cc796fc069f9bb820318e5909000
# Parent  d97ff93a71f8588f64e66128c800fda37812fb87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb

diff -r d97ff93a71f8 -r ed2c532794c1 bbduk.xml
--- a/bbduk.xml	Tue May 30 09:00:52 2023 +0000
+++ b/bbduk.xml	Tue Aug 27 10:13:47 2024 +0000
@@ -4,10 +4,10 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="edam_ontology"/>
+    <expand macro="bio.tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#import re
 
 #if str($input_type_cond.input_type) in ['single', 'pair']:
     #set read1 = $input_type_cond.read1
@@ -25,17 +25,15 @@
     #end if
 #else:
     #set read1 = $input_type_cond.reads_collection['forward']
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
     ## bbduk uses the file extension to determine the input format.
-    #set ext = $read1_identifier + '.fastq'
+    #set ext = '.fastq'
     #if $read1.ext.endswith('.gz'):
         #set ext = $ext + '.gz'
     #end if
-    #set read1_file = $read1_identifier + $ext
+    #set read1_file = 'forward' + $ext
     ln -s '${read1}' '${read1_file}' &&
     #set read2 = $input_type_cond.reads_collection['reverse']
-    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
-    #set read2_file = $read2_identifier + $ext
+    #set read2_file = 'reverse' + $ext
     ln -s '${read2}' '${read2_file}' &&
 #end if
 
@@ -156,11 +154,11 @@
             </param>
             <when value="no_reference"/>
             <when value="files">
-                <param name="reference" type="data" format="fasta,fasta.gz" multiple="true" optional="false" label="Select one or more fasta file"/>
+                <param name="reference" type="data" format="fasta,fasta.gz" optional="false" label="Select one or more fasta file" multiple="true"/>
                 <expand macro="ktrim_cond"/>
             </when>
             <when value="keywords">
-                <param name="reference"  type="select" multiple="true" optional="false" label="Select one or more keywords">
+                <param name="reference" type="select" optional="false" label="Select one or more keywords" multiple="true">
                     <option value="adapters">adapters</option>
                     <option value="artifacts">artifacts</option>
                     <option value="phix">phix</option>
@@ -173,34 +171,34 @@
             </when>
         </conditional>
         <section name="advanced_options" title="Advanced options" expanded="false">
-            <param argument="k" type="integer" value="27" min="1" label="Kmer length used for finding contaminants"/>
+            <param argument="k" type="integer" min="1" value="27" label="Kmer length used for finding contaminants"/>
             <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/>
             <param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/>
-            <param argument="minkmerhits" type="integer" value="1" min="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
-            <param argument="minkmerfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
-            <param argument="mincovfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
-            <param argument="hammingdistance" type="integer" value="0" min="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
-            <param argument="qhdist" type="integer" value="0" min="0" label="Hamming distance for query kmers"/>
-            <param argument="editdistance" type="integer" value="0" min="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
+            <param argument="minkmerhits" type="integer" min="1" value="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
+            <param argument="minkmerfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
+            <param argument="mincovfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
+            <param argument="hammingdistance" type="integer" min="0" value="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
+            <param argument="qhdist" type="integer" min="0" value="0" label="Hamming distance for query kmers"/>
+            <param argument="editdistance" type="integer" min="0" value="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
             <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/>
             <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/>
             <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/>
             <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/>
             <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/>
         </section>
-        <param name="outputs_select"  type="select" multiple="true" optional="false" label="Specify outputs">
+        <param name="outputs_select" type="select" optional="false" label="Specify outputs" multiple="true">
             <option value="outu">Unmatched</option>
             <option value="outm">Matched</option>
             <option value="outs">Single</option>
         </param>
         <conditional name="output_stats_cond">
-            <param name="output_stats"  type="select" label="Output statistics?">
+            <param name="output_stats" type="select" label="Output statistics?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>
             <when value="yes">
-                <param name="output_stats_select"  type="select" multiple="true" optional="false" label="Specify statistics outputs">
+                <param name="output_stats_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
                     <option value="stats">Statistics about which contamininants were detected</option>
                     <option value="ref">Statistics on a per-reference-file basis</option>
                     <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option>
@@ -209,13 +207,13 @@
             </when>
         </conditional>
         <conditional name="output_hists_cond">
-            <param name="output_hists"  type="select" label="Output histograms?">
+            <param name="output_hists" type="select" label="Output histograms?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>
             <when value="yes">
-                <param name="output_hists_select"  type="select" multiple="true" optional="false" label="Specify statistics outputs">
+                <param name="output_hists_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
                     <option value="bhist">Base composition histogram by position</option>
                     <option value="quhist">Quality histogram by position</option>
                     <option value="quchist">Count of bases with each quality value</option>
@@ -231,7 +229,7 @@
     </inputs>
     <outputs>
         <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
-            <filter>str(outputs_select).find('outu') >= 0</filter>
+            <filter>str(outputs_select).find('outu') &gt;= 0</filter>
             <filter>'outu' in outputs_select</filter>
         </data>
         <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
@@ -352,4 +350,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-
diff -r d97ff93a71f8 -r ed2c532794c1 macros.xml
--- a/macros.xml	Tue May 30 09:00:52 2023 +0000
+++ b/macros.xml	Tue Aug 27 10:13:47 2024 +0000
@@ -1,21 +1,31 @@
 <macros>
-    <token name="@TOOL_VERSION@">39.01</token>
+    <token name="@TOOL_VERSION@">39.08</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>
-            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
-            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
+            <edam_topic>topic_0622</edam_topic>
+            <!-- Genomics -->
+            <edam_topic>topic_0091</edam_topic>
+            <!-- Bioinformatics -->
         </edam_topics>
         <edam_operations>
-            <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
-            <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
+            <edam_operation>operation_0496</edam_operation>
+            <!-- Global alignment -->
+            <edam_operation>operation_0491</edam_operation>
+            <!-- Pairwise sequence alignment -->
         </edam_operations>
     </xml>
+    <xml name="bio.tools">
+        <xrefs>
+            <xref type="bio.tools">bbtools</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
-            <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
+            <requirement type="package" version="1.20">samtools</requirement>
+            <!-- automatic solving installs 1.6 in some cases, instead -->
         </requirements>
     </xml>
     <macro name="dbKeyActionsBBMap">
@@ -57,7 +67,7 @@
                 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
             </when>
             <when value="paired">
-                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
+                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Collection of fastqsanger paired read files" collection_type="paired"/>
             </when>
         </conditional>
     </macro>
@@ -82,18 +92,18 @@
     </macro>
     <macro name="ktrim_cond">
         <conditional name="ktrim_cond">
-            <param name="ktrim_select"  type="select" label="Trim reads to remove bases matching reference kmers?">
+            <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>
             <when value="yes">
-                <param argument="ktrim"  type="select" label="Select trimming position">
+                <param argument="ktrim" type="select" label="Select trimming position">
                     <option value="r">Trim to the right</option>
                     <option value="l">Trim to the left</option>
                 </param>
                 <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
-             </when>
+            </when>
         </conditional>
     </macro>
     <xml name="citations">
@@ -104,4 +114,3 @@
         </citations>
     </xml>
 </macros>
-
diff -r d97ff93a71f8 -r ed2c532794c1 test-data/cv_output.gff
--- a/test-data/cv_output.gff	Tue May 30 09:00:52 2023 +0000
+++ b/test-data/cv_output.gff	Tue Aug 27 10:13:47 2024 +0000
@@ -1,18 +1,18 @@
-##gff-version
-#BBMapVersion
+##gff-version 3
+#BBMapVersion	39.08
 #ploidy	2
 #rarity	1.00000
 #minAlleleFraction	0.1000
 #reads	2207
 #pairedReads	0
 #properlyPairedReads	0
-#readLengthAvg
+#readLengthAvg	145.46
 #properPairRate	0.0000
-#totalQualityAvg
-#mapqAvg
-#reference
+#totalQualityAvg	36.5800
+#mapqAvg	43.35
+#reference	/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
 #seqid	source	type	start	end	score	strand	phase	attributes
-NC_002945.4	.	sequence_variant_obs	976327	976327
-NC_002945.4	.	sequence_variant_obs	1501932	1501932
-NC_002945.4	.	sequence_variant_obs	3380579	3380579
-NC_002945.4	.	sequence_variant_obs	3646293	3646293
+NC_002945.4	.	sequence_variant_obs	976327	976327	0.87	+	.	ID=SUB T
+NC_002945.4	.	sequence_variant_obs	1501932	1501932	0.92	+	.	ID=SUB C
+NC_002945.4	.	sequence_variant_obs	3380579	3380579	0.92	+	.	ID=SUB G
+NC_002945.4	.	sequence_variant_obs	3646293	3646293	0.89	+	.	ID=SUB A
diff -r d97ff93a71f8 -r ed2c532794c1 test-data/cv_output.txt
--- a/test-data/cv_output.txt	Tue May 30 09:00:52 2023 +0000
+++ b/test-data/cv_output.txt	Tue Aug 27 10:13:47 2024 +0000
@@ -1,18 +1,18 @@
-#fileformat
-#BBMapVersion
+#fileformat	Var_1.3
+#BBMapVersion	39.08
 #ploidy	2
 #rarity	1.00000
 #minAlleleFraction	0.1000
 #reads	2207
 #pairedReads	0
 #properlyPairedReads	0
-#readLengthAvg
-#properPairRate
-#totalQualityAvg
-#mapqAvg
-#reference
+#readLengthAvg	145.46
+#properPairRate	0.0000
+#totalQualityAvg	36.5800
+#mapqAvg	43.35
+#reference	/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
 #scaf	start	stop	type	call	r1p	r1m	r2p	r2m	paired	lengthSum	mapq	mapqMax	baseq	baseqMax	edist	edistMax	id	idMax	cov	minusCov	nearbyVarCount	flagged	contigEndDist	phredScore	readCount	alleleFraction	revisedAF	strandRatio	baseqAvg	mapqAvg	edistAvg	identityAvg	edistScore	identityScore	qualityScore	pairedScore	biasScore	coverageScore	homopolymerScore	score
-0	976326	976327	SUB	T
-0	1501931	1501932	SUB	C
-0	3380578	3380579	SUB	G
-0	3646292	3646293	SUB	A
+0	976326	976327	SUB	T	2	0	0	0	0	292	77	40	48	24	111	65	1930	972	0	-1	0	0	0	22.21	2	1	1	0.5000	24	38.50	55.50	965	0.9972	0.9932	0.7489	0.9800	0.9737	0.7143	1	0.8725
+0	1501931	1501932	SUB	C	0	2	0	0	0	292	88	44	64	39	74	38	1986	993	0	-1	0	0	0	27.20	2	1	1	0.5000	32	44	37	993	0.9851	0.9994	0.9831	0.9800	0.9737	0.7143	1	0.9202
+0	3380578	3380579	SUB	G	0	2	0	0	0	289	87	44	75	38	105	63	1986	993	0	-1	0	0	0	27.85	2	1	1	0.5000	37.50	43.50	52.50	993	0.9968	0.9994	0.9972	0.9800	0.9737	0.7143	1	0.9250
+0	3646292	3646293	SUB	A	1	1	0	0	0	291	86	44	76	38	44	31	1986	993	0	-1	0	0	0	23.34	2	1	1	1	38	43	22	993	0.7996	0.9994	0.9975	0.9800	0.9747	0.7143	1	0.8853
diff -r d97ff93a71f8 -r ed2c532794c1 test-data/cv_output.vcf
--- a/test-data/cv_output.vcf	Tue May 30 09:00:52 2023 +0000
+++ b/test-data/cv_output.vcf	Tue Aug 27 10:13:47 2024 +0000
@@ -1,16 +1,16 @@
 ##fileformat=VCFv4.2
-##BBMapVersion=
+##BBMapVersion=39.08
 ##ploidy=2
 ##rarity=1.00000
 ##minallelefraction=0.10000
 ##reads=2207
 ##pairedReads=0
 ##properlyPairedReads=0
-##readLengthAvg=
+##readLengthAvg=145.462
 ##properPairRate=0.00000
-##totalQualityAvg=
+##totalQualityAvg=36.580
 ##mapqAvg=43.348
-##reference=
+##reference=/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
 ##contig=<ID=NC_002945.4,length=7000>
 ##FILTER=<ID=FAIL,Description="Fail">
 ##FILTER=<ID=PASS,Description="Pass">
@@ -53,8 +53,8 @@
 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	
-NC_002945.4	976327	.	N	T	22.21	PASS	SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
-NC_002945.4	1501932	.	N	C	27.20	PASS	SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
-NC_002945.4	3380579	.	N	G	27.85	PASS	SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
-NC_002945.4	3646293	.	N	A	23.34	PASS	SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	dataset_4f1db038-76fe-46bc-a222-dfc4894a8ff2.dat
+NC_002945.4	976327	.	N	T	22.21	PASS	SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1:1:0:0:0.9980:22.21:PASS
+NC_002945.4	1501932	.	N	C	27.20	PASS	SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1:1:0:0:0.9980:27.20:PASS
+NC_002945.4	3380579	.	N	G	27.85	PASS	SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1:1:0:0:0.9980:27.85:PASS
+NC_002945.4	3646293	.	N	A	23.34	PASS	SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1:1:0:0:1:23.34:PASS
diff -r d97ff93a71f8 -r ed2c532794c1 test-data/cv_qualityhist_output.tabular
--- a/test-data/cv_qualityhist_output.tabular	Tue May 30 09:00:52 2023 +0000
+++ b/test-data/cv_qualityhist_output.tabular	Tue Aug 27 10:13:47 2024 +0000
@@ -1,8 +1,8 @@
 #BaseQualityHist
-#Vars
-#Mean
-#Median
-#Mode
+#Vars	4
+#Mean	32.75
+#Median	32
+#Mode	32
 #Quality	AvgCount	MaxCount
 0	0	0
 1	0	0
diff -r d97ff93a71f8 -r ed2c532794c1 test-data/cv_scorehist_output.tabular
--- a/test-data/cv_scorehist_output.tabular	Tue May 30 09:00:52 2023 +0000
+++ b/test-data/cv_scorehist_output.tabular	Tue Aug 27 10:13:47 2024 +0000
@@ -1,8 +1,8 @@
 #ScoreHist
-#Vars
-#Mean
-#Median
-#Mode
+#Vars	4
+#Mean	24.75
+#Median	23
+#Mode	27
 #Quality	Count
 0	0
 1	0
diff -r d97ff93a71f8 -r ed2c532794c1 test-data/cv_zygosityhist_output.tabular
--- a/test-data/cv_zygosityhist_output.tabular	Tue May 30 09:00:52 2023 +0000
+++ b/test-data/cv_zygosityhist_output.tabular	Tue Aug 27 10:13:47 2024 +0000
@@ -1,7 +1,7 @@
 #ZygoHist
-#Vars
-#Mean
-#HomozygousFraction
+#Vars	4
+#Mean	2.000
+#HomozygousFraction	1.000
 #Zygosity	Count
 0	0
 1	0