Mercurial > repos > dfornika > tetyper
changeset 7:e479272681a6 draft
Uploaded
| author | dfornika |
|---|---|
| date | Tue, 26 Nov 2019 19:48:25 +0000 |
| parents | 8fc05ce77eb7 |
| children | 010a346ee927 |
| files | tetyper.xml |
| diffstat | 1 files changed, 36 insertions(+), 27 deletions(-) [+] |
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--- a/tetyper.xml Tue Nov 26 00:07:23 2019 +0000 +++ b/tetyper.xml Tue Nov 26 19:48:25 2019 +0000 @@ -47,6 +47,15 @@ <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log"/> </outputs> <tests> + <test> + <param name="reference" value="Tn4401b-1.fasta" /> + <conditional name="collection_paired"> + <param name="selector" value="paired" /> + <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> + <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> + <output name="summary" file="output_summary.txt" /> + </conditional> + </test> </tests> <help> <![CDATA[ @@ -58,33 +67,33 @@ TETyper will produce a tab-seperated output file with the following outputs: -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Column | Description | -+==========================+==========================================================================================================================================+ -| Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Structural_variant | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| SNPs_homozygous | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| SNPs_heterozygous | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Heterozygous_SNP_counts | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| SNP_variant | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Combined_variant | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Left_flanks | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Right_flanks | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Left_flank_counts | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| Right_flank_counts | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ -| X_Y_presence | | -+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Column | Description | ++==========================+==================================================================================================================================================================================================================================================+ +| Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Structural_variant | If --struct_profiles is specified and the pattern of deletions above corresponds to one of these profiles, then the profile name is given, otherwise "unknown". | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| SNPs_homozygous | A list of homozygous SNPs identified, or "none". | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| SNPs_heterozygous | A list of heterozygous SNPs identified, or "none". | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Heterozygous_SNP_counts | For each heterozygous SNP, the number of reads supporting the reference and alternative calls, or "none" if there are no heterozygous SNPs. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| SNP_variant | If --snp_profiles is specified and the pattern of homozygous and heterozygous SNPs corresponds to one of these profiles, then the profile name is given. Otherwise "unknown". | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Combined_variant | Single name combining Structural_variant and SNP_variant, separated by "-". | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Left_flanks | A list of distinct sequences passing quality filters that flank the start position of the reference. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Right_flanks | A list of distinct sequences passing quality filters that flank the end position of the reference. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Left_flank_counts | The number of high quality reads supporting each of the left flanking sequences. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Right_flank_counts | The number of high quality reads supporting each of the right flanking sequences. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| X_Y_presence | If --show_region is specified as --show_region X-Y, this column shows 1 if the entirety of that region is classified as present (i.e. no overlap with deleted regions), or 0 otherwise. If --show_region is unspecified, this column is omitted. | ++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ ]]> </help>