generic-non-segmented-viral-variant-calling/main

ID	Name	Description	Type
Fasta reference genome	Fasta reference genome	A reference sequence for your virus	File
Minimum quality score to consider base for variant calling	Minimum quality score to consider base for variant calling	The same threshold applies for variant calling and consensus generation.	int
Paired collection of sequencing data	Paired collection of sequencing data	The PE sequencing data for your batch of samples organized as a list of pairs collection	File[]
Primer scheme (optional)	Primer scheme (optional)	If provided, indicates ampliconic data and will trigger primer trimming and removal of reads that extend beyond amplicon boundaries. Please make sure the scheme matches your reference sequence and that the format of the dataset is set to bed!	File?
Reference annotation	Reference annotation	Needs to be provided in GTF format. Please make sure it is matching your reference genome sequence!	File
Supporting read fraction to call variant	Supporting read fraction to call variant	Specify what fraction of variant-supporting reads is minimally needed at a site to call that variant (a floating point value between 0.05 and 0.25).	float

ID	Name	Description
6	fastp: Trimmed Illumina Reads	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy0
7	SnpEff build:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0
8	Map parameter value	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
9	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
10	Calculate numeric parameter value	toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0
11	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19
12	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
13	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0
14	QualiMap BamQC	toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0
15	Realign reads	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
16	Filter failed datasets	__FILTER_FAILED_DATASETS__
17	ivar trim	toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.4+galaxy1
18	Flatten collection	__FLATTEN__
19	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
20	Quality Control Report	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
21	ivar variants	toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.4+galaxy0
22	ivar consensus	toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.4+galaxy0
23	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0
24	Text transformation	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2
25	Remove annotations for suspicious transcripts	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2
26	Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2
27	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
28	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

ID	Name	Description	Type
Processed mapped reads (filtered and realigned)	Processed mapped reads (filtered and realigned)	n/a	File
Processed mapped reads (filtered, realigned, primers trimmed	Processed mapped reads (filtered, realigned, primers trimmed	n/a	File
Quality control report	Quality control report	n/a	File
Per-sample consensus genomes	Per-sample consensus genomes	n/a	File
SnpEff-annotated variants	SnpEff-annotated variants	n/a	File
Combined consensus genomes for all samples	Combined consensus genomes for all samples	n/a	File
Combined variant report for all samples	Combined variant report for all samples	n/a	File