# HG changeset patch
# User jjohnson
# Date 1529013033 14400
# Node ID d9fad18ffdb1b7b76f76c25278aeb63d61db6b07
# Parent  9e83cc05d384b73ed5c2f19660dde78969fa4a54
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty

diff -r 9e83cc05d384 -r d9fad18ffdb1 ._ensembl_variant_report.py
Binary file ._ensembl_variant_report.py has changed
diff -r 9e83cc05d384 -r d9fad18ffdb1 ._ensembl_variant_report.xml
Binary file ._ensembl_variant_report.xml has changed
diff -r 9e83cc05d384 -r d9fad18ffdb1 ._ensemblref.py
Binary file ._ensemblref.py has changed
diff -r 9e83cc05d384 -r d9fad18ffdb1 ensembl_variant_report.py
--- 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('|'))
diff -r 9e83cc05d384 -r d9fad18ffdb1 ensembl_variant_report.xml
--- 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
diff -r 9e83cc05d384 -r d9fad18ffdb1 ensemblref.py
diff -r 9e83cc05d384 -r d9fad18ffdb1 test-data/._.DS_Store
Binary file test-data/._.DS_Store has changed