Mercurial > repos > nml > filter_stats
changeset 0:89c3ba37711c draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:31:08 -0400 |
| parents | |
| children | 2fbea749a1d1 |
| files | filter-stats.xml test-data/filter-stats-in.tsv test-data/filter-stats-out.tabular |
| diffstat | 3 files changed, 66 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter-stats.xml Tue Aug 27 12:31:08 2019 -0400 @@ -0,0 +1,48 @@ +<tool id="filterstat" name="Filter Stats" version ="1.8.2"> + <description>Identify number of positions excluded based on filtered status</description> + <requirements> + <requirement type="package" version="1.8.2">snvphyl-tools</requirement> + </requirements> + <command detect_errors="exit_code"> + filter-stats.pl -i $tabfile + #if $summary: + -a + #end if + > $out + </command> + <inputs> + <param name="tabfile" type="data" label="SNV-alignment positions tab delimited file" format="tabular"/> + <param name="summary" type="select" display="checkboxes" label="Summary Options" multiple="true"> + <option value="invalids">Include all entries marked as 'filtered-invalid'</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="out" /> + </outputs> + <tests> + <test> + <param name="tabfile" value="filter-stats-in.tsv" /> + <output name="out" file="filter-stats-out.tabular" /> + </test> + </tests> + + <help> +What it does +============ + +This script prints a stat summary of the number of N's and -'s found in the SNV-alignment positions tab delimited file. + + +Usage +===== + +**Parameters** + - input - The SNV-alignment positions tab delimited file + + +**Options** + - -all When this option is set, the summary will include all the entries marked as 'filtered-invalid' + </help> +<citations> +</citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filter-stats-in.tsv Tue Aug 27 12:31:08 2019 -0400 @@ -0,0 +1,3 @@ +#Chromosome Position Status Reference query B +chr 5 valid A T A +chr 10 filtered-coverage A G -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filter-stats-out.tabular Tue Aug 27 12:31:08 2019 -0400 @@ -0,0 +1,15 @@ +Chromosome Genomes +chr ALL B query +Total number of N's and -'s 1 1 0 +Total percent of N's and -'s 50.00 50.00 0.00 +Total number of unfiltered variants in chromosome: 2 + +================= Filter Summary Statistics ===================== +Number of sites used to generate phylogeny: 1 +Total number of sites identified: 2 +Number of sites filtered: 1 +Percentage of sites filtered: 50.00 +Coverage filtered: 1 +mpileup filtered: 0 +Invalid filtered: Invalid positions not analyzed. Please use -a flag to analyze. +