Mercurial > repos > jjohnson > ensembl_variant_report
changeset 6:d9fad18ffdb1 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
| author | jjohnson |
|---|---|
| date | Thu, 14 Jun 2018 17:50:33 -0400 |
| parents | 9e83cc05d384 |
| children | d5cb252c68da |
| files | ._ensembl_variant_report.py ._ensembl_variant_report.xml ._ensemblref.py ensembl_variant_report.py ensembl_variant_report.xml ensemblref.py test-data/._.DS_Store |
| diffstat | 6 files changed, 18 insertions(+), 11 deletions(-) [+] |
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--- a/ensembl_variant_report.py Mon Feb 06 09:25:43 2017 -0500 +++ b/ensembl_variant_report.py Thu Jun 14 17:50:33 2018 -0400 @@ -113,13 +113,15 @@ alt_list = alts.split(',') pos = int(pos) qual = float(qual) + dp = None + dpr = None for info_item in info.split(';'): if info_item.find('=') < 0: continue (key, val) = info_item.split('=', 1) if key == 'DP': dp = int(val) if key == 'DPR': - dpr = dpr = [int(x) for x in val.split(',')] + dpr = [int(x) for x in val.split(',')] if key in ['EFF','ANN']: for effect in val.split(','): if options.debug: print >> sys.stderr, "\n%s" % (effect.split('|'))
--- a/ensembl_variant_report.xml Mon Feb 06 09:25:43 2017 -0500 +++ b/ensembl_variant_report.xml Thu Jun 14 17:50:33 2018 -0400 @@ -79,13 +79,17 @@ </conditional> <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/> <section name="filter" expanded="false" title="Filter Options"> - <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report"/> - <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report"/> + <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report" + help="If a value is entered, ignore variants with DP INFO field less than this value"/> + <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report" + help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/> </section> <section name="report" expanded="false" title="Report Options"> - <param name="readthrough" type="integer" value="" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/> - <param name="leading_aa" type="integer" value="" optional="true" min="0" label="Number of Amino Acids prior to variant to display"/> - <param name="trailing_aa" type="integer" value="" optional="true" min="0" label="Number of Amino Acids following the variant to display"/> + <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/> + <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display" + help="Ignored for frame shifts"/> + <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display" + help="Ignored for frame shifts"/> </section> </inputs> @@ -99,7 +103,7 @@ <param name="ref_source" value="history"/> <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> - <output name="output_file"> + <output name="output"> <assert_contents> <has_text text="MGGQ_A_SASNSFSRLH" /> <not_has_text text="*REDHAAGPEA" /> @@ -112,7 +116,7 @@ <param name="ref_source" value="history"/> <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> - <output name="output_file"> + <output name="output"> <assert_contents> <has_text text="MGGQ_A_SASNSFSRLH" /> <not_has_text text="*REDHAAGPEA" /> @@ -126,7 +130,7 @@ <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> <param name="readthrough" value="1"/> - <output name="output_file"> + <output name="output"> <assert_contents> <has_text text="MGGQ_A_SASNSFSRLH" /> <has_text text="*REDHAAGPEA" /> @@ -141,7 +145,7 @@ <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> <param name="min_depth" value="100"/> <param name="min_freq" value=".80"/> - <output name="output_file"> + <output name="output"> <assert_contents> <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" /> <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" /> @@ -160,7 +164,7 @@ <param name="transcript_column" value="7"/> <param name="dp_column" value="8"/> <param name="dpr_column" value="9"/> - <output name="output_file"> + <output name="output"> <assert_contents> <has_text text="MGGQ_A_SASNSFSRLH" /> <not_has_text text="*REDHAAGPEA" /> @@ -174,6 +178,7 @@ Input can be a snpEff vcf file using either ANN or EFF annotations. Alternatively, the input can be a tabular file that has columns: + - pos - ref - alt