# HG changeset patch # User iuc # Date 1691166884 0 # Node ID e8971ca74398fd55feb35b2c4b630e728fbea8b4 # Parent 029d90b0c4f67b7786fe61d249cad3cf29d52d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit 2189ba7df6d90ed10c6fdb07df93545f8f282339 diff -r 029d90b0c4f6 -r e8971ca74398 frameshift_deletions_checks.xml --- a/frameshift_deletions_checks.xml Fri Jul 14 22:07:22 2023 +0000 +++ b/frameshift_deletions_checks.xml Fri Aug 04 16:34:44 2023 +0000 @@ -7,7 +7,7 @@ smallgenomeutilities - + frameshift_deletions_checks --version + + + + + + + + + + + @@ -71,6 +85,7 @@ + @@ -82,17 +97,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -100,41 +175,59 @@ + + + + + + + + + + + + + + + + `_. +The smallgenomeutilities are part of the `V-pipe workflow for analysing NGS data of short viral genomes `_. Columns signification: ---------------------- +* *ref_id* / *cons_id*: name of the sequence in the reference and consensus +* *start_position* / *length*: location of the variant +* *VARIANT*: one of: "insertion", "deletion", "stopgain" or "stoploss" * *gene_region*: Gene in which the deletion is found according to ``--genes`` argument; * *reads_all*: Total number of reads covering the indel; * *reads_fwd*: Total number of forward reads covering the indel; * *reads_rev*: Total number of reverse reads covering the indel; -* *deletions/insertions*: Number of reads supporting the deletion/insertion; -* *freq_del/freq_insert*: Fraction of reads supporting the deletion/insertion; +* *deletions* / *insertions*: Number of reads supporting the deletion/insertion; +* *freq_del* / *freq_insert*: Fraction of reads supporting the deletion/insertion; * *matches_ref*: number of reads that matche with the reference base; * *pos_critical_inserts*: Start positions of insertions in the same gene_region that occur in > 40% of reads; * *pos_critical_dels*: Start positions of deletions in the same gene_region that occur in > 40% of reads; * *homopolymeric*: True if either around the start or end position of the deletion three bases are the same, which may have caused the polymerase to skip during reverse transcription of viral RNA to cDNA, e.g. AATAG; * *ref_base*: base in the reference genome; -* *indel_position_english*: english sentence describing the indel; -* *indel_diagnosis*: english sentence with the indel diagnosis; -* *orf1ab*: CDS ID for the full Orf1ab CDS, comprising the ribosomal shift. In the GFF this CDS should consist of 2 entries with the same CDS ID due to the parital overlap caused by the ribosomal shift at translation time +* *variant_position_english*: english sentence describing the indel or stop; +* *variant_diagnosis*: english sentence with the indel diagnosis ]]> diff -r 029d90b0c4f6 -r e8971ca74398 macros.xml --- a/macros.xml Fri Jul 14 22:07:22 2023 +0000 +++ b/macros.xml Fri Aug 04 16:34:44 2023 +0000 @@ -1,6 +1,6 @@ - 0.3.9 - 1 + 0.4.0 + 0 21.09 diff -r 029d90b0c4f6 -r e8971ca74398 test-data/consensus.bcftools.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus.bcftools.chain Fri Aug 04 16:34:44 2023 +0000 @@ -0,0 +1,3 @@ +chain 29903 NC_045512.2 29903 + 0 29903 NC_045512.2 29903 + 0 29903 1 +29903 + diff -r 029d90b0c4f6 -r e8971ca74398 test-data/consensus.bcftools_nogap.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus.bcftools_nogap.chain Fri Aug 04 16:34:44 2023 +0000 @@ -0,0 +1,6 @@ +chain 29899 NC_045512.2 29903 + 0 29903 NC_045512.2 29899 + 0 29899 1 +5599 2 0 +3138 1 0 +10059 1 0 +11103 + diff -r 029d90b0c4f6 -r e8971ca74398 test-data/consensus.bcftools_nogap.fasta.gz Binary file test-data/consensus.bcftools_nogap.fasta.gz has changed