Mercurial > repos > iuc > bbtools_bbmerge

changeset 6:cab19c0452c4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:15:19 +0000
parents 1af48f9cc27b
children
files bbmerge.xml macros.xml test-data/cv_output.gff test-data/cv_output.txt test-data/cv_output.vcf test-data/cv_qualityhist_output.tabular test-data/cv_scorehist_output.tabular test-data/cv_zygosityhist_output.tabular
diffstat 8 files changed, 57 insertions(+), 60 deletions(-) [+]
line wrap: on
line diff
--- a/bbmerge.xml	Sat May 18 19:12:59 2024 +0000
+++ b/bbmerge.xml	Tue Aug 27 10:15:19 2024 +0000
@@ -98,7 +98,6 @@
 ]]></command>
     <inputs>
         <expand macro="input_type_cond"/>
-        
         <section name="qt_options" title="Quality and trimming options">
             <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
                 <option value="f" selected="true">No trimming</option>
@@ -110,7 +109,6 @@
             <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
         </section>
-        
         <section name="merge_options" title="Merging parameters">
             <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
                 <option value="xstrict">max strict</option>
@@ -128,16 +126,13 @@
             <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
             <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
             <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
-            
             <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
             <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
-            
             <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
             <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
             <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
             <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
-            
             <conditional name="adapters">
                 <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
                     <option value="wout_adapters" selected="true">No</option>
@@ -149,7 +144,6 @@
                     <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
                 </when>
             </conditional>
-
             <conditional name="merge_mode">
                 <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
                     <option value="Ratio mode" selected="true">Ratio mode</option>
@@ -253,4 +247,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-
--- a/macros.xml	Sat May 18 19:12:59 2024 +0000
+++ b/macros.xml	Tue Aug 27 10:15:19 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>
-
--- a/test-data/cv_output.gff	Sat May 18 19:12:59 2024 +0000
+++ b/test-data/cv_output.gff	Tue Aug 27 10:15:19 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
--- a/test-data/cv_output.txt	Sat May 18 19:12:59 2024 +0000
+++ b/test-data/cv_output.txt	Tue Aug 27 10:15:19 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
--- a/test-data/cv_output.vcf	Sat May 18 19:12:59 2024 +0000
+++ b/test-data/cv_output.vcf	Tue Aug 27 10:15:19 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
--- a/test-data/cv_qualityhist_output.tabular	Sat May 18 19:12:59 2024 +0000
+++ b/test-data/cv_qualityhist_output.tabular	Tue Aug 27 10:15:19 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
--- a/test-data/cv_scorehist_output.tabular	Sat May 18 19:12:59 2024 +0000
+++ b/test-data/cv_scorehist_output.tabular	Tue Aug 27 10:15:19 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
--- a/test-data/cv_zygosityhist_output.tabular	Sat May 18 19:12:59 2024 +0000
+++ b/test-data/cv_zygosityhist_output.tabular	Tue Aug 27 10:15:19 2024 +0000
@@ -1,7 +1,7 @@
 #ZygoHist
-#Vars
-#Mean
-#HomozygousFraction
+#Vars	4
+#Mean	2.000
+#HomozygousFraction	1.000
 #Zygosity	Count
 0	0
 1	0