# HG changeset patch
# User iuc
# Date 1724753685 0
# Node ID 7e041c120b9692c4a3c743a85728d06c8bce69ac
# Parent  66b138a2e74c6c00321573b5eab38c97dad06e1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb

diff -r 66b138a2e74c -r 7e041c120b96 callvariants.xml
--- a/callvariants.xml	Sat May 18 19:13:20 2024 +0000
+++ b/callvariants.xml	Tue Aug 27 10:14:45 2024 +0000
@@ -39,7 +39,7 @@
     <inputs>
         <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/>
         <expand macro="reference_source_cond"/>
-        <param name="ploidy" type="integer" value="1" min="1" label="Ploidy" help="See help section below"/>
+        <param name="ploidy" type="integer" min="1" value="1" label="Ploidy" help="See help section below"/>
         <param name="output_format" type="select" label="Select output format">
             <option value="vcf" selected="true">vcf</option>
             <option value="gff">gff</option>
@@ -73,7 +73,7 @@
             <param name="output_variant_score_hist" value="yes"/>
             <param name="output_zygosity_hist" value="yes"/>
             <param name="output_quality_hist" value="yes"/>
-            <output name="output" file="cv_output.vcf" ftype="vcf" compare="contains"/>
+            <output name="output" file="cv_output.vcf" ftype="vcf" compare="diff" lines_diff="4"/>
             <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/>
             <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/>
             <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/>
@@ -82,13 +82,13 @@
             <param name="input" value="cv_input.bam" ftype="bam"/>
             <param name="ploidy" value="2"/>
             <param name="output_format" value="gff"/>
-            <output name="output" file="cv_output.gff" ftype="gff" compare="contains"/>
+            <output name="output" file="cv_output.gff" ftype="gff" compare="contains" lines_diff="2"/>
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="cv_input.bam" ftype="bam"/>
             <param name="ploidy" value="2"/>
             <param name="output_format" value="txt"/>
-            <output name="output" file="cv_output.txt" ftype="txt" compare="contains"/>
+            <output name="output" file="cv_output.txt" ftype="txt" compare="contains" lines_diff="2"/>
         </test>
     </tests>
     <help>
@@ -108,4 +108,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-
diff -r 66b138a2e74c -r 7e041c120b96 macros.xml
--- a/macros.xml	Sat May 18 19:13:20 2024 +0000
+++ b/macros.xml	Tue Aug 27 10:14:45 2024 +0000
@@ -1,15 +1,19 @@
 <macros>
-    <token name="@TOOL_VERSION@">39.06</token>
-    <token name="@VERSION_SUFFIX@">2</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">
@@ -20,7 +24,8 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
-            <requirement type="package" version="1.19.2">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">
@@ -62,7 +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>
@@ -87,18 +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">
@@ -109,4 +114,3 @@
         </citations>
     </xml>
 </macros>
-
diff -r 66b138a2e74c -r 7e041c120b96 test-data/cv_output.gff
--- a/test-data/cv_output.gff	Sat May 18 19:13:20 2024 +0000
+++ b/test-data/cv_output.gff	Tue Aug 27 10:14:45 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 66b138a2e74c -r 7e041c120b96 test-data/cv_output.txt
--- a/test-data/cv_output.txt	Sat May 18 19:13:20 2024 +0000
+++ b/test-data/cv_output.txt	Tue Aug 27 10:14:45 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 66b138a2e74c -r 7e041c120b96 test-data/cv_output.vcf
--- a/test-data/cv_output.vcf	Sat May 18 19:13:20 2024 +0000
+++ b/test-data/cv_output.vcf	Tue Aug 27 10:14:45 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 66b138a2e74c -r 7e041c120b96 test-data/cv_qualityhist_output.tabular
--- a/test-data/cv_qualityhist_output.tabular	Sat May 18 19:13:20 2024 +0000
+++ b/test-data/cv_qualityhist_output.tabular	Tue Aug 27 10:14:45 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 66b138a2e74c -r 7e041c120b96 test-data/cv_scorehist_output.tabular
--- a/test-data/cv_scorehist_output.tabular	Sat May 18 19:13:20 2024 +0000
+++ b/test-data/cv_scorehist_output.tabular	Tue Aug 27 10:14:45 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 66b138a2e74c -r 7e041c120b96 test-data/cv_zygosityhist_output.tabular
--- a/test-data/cv_zygosityhist_output.tabular	Sat May 18 19:13:20 2024 +0000
+++ b/test-data/cv_zygosityhist_output.tabular	Tue Aug 27 10:14:45 2024 +0000
@@ -1,7 +1,7 @@
 #ZygoHist
-#Vars
-#Mean
-#HomozygousFraction
+#Vars	4
+#Mean	2.000
+#HomozygousFraction	1.000
 #Zygosity	Count
 0	0
 1	0