changeset 12:7a418148319d draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/read2mut.py	Mon Feb 15 21:53:24 2021 +0000
+++ b/read2mut.py	Tue Feb 16 07:08:25 2021 +0000
@@ -46,7 +46,11 @@
     parser.add_argument('--sscsJson',
                         help='JSON file with SSCS counts collected by mut2sscs.py.')
     parser.add_argument('--outputFile',
-                        help='Output xlsx file of mutation details.')
+                        help='Output xlsx file with summary of mutations.')
+    parser.add_argument('--outputFile2',
+                        help='Output xlsx file with allele frequencies of mutations.')
+    parser.add_argument('--outputFile3',
+                        help='Output xlsx file with examples of the tier classification.')
     parser.add_argument('--thresh', type=int, default=0,
                         help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.')
     parser.add_argument('--phred', type=int, default=20,
@@ -72,6 +76,8 @@
     json_file = args.inputJson
     sscs_json = args.sscsJson
     outfile = args.outputFile
+    outfile2 = args.outputFile2
+    outfile3 = args.outputFile3
     thresh = args.thresh
     phred_score = args.phred
     trim = args.trim

--- a/read2mut.xml	Mon Feb 15 21:53:24 2021 +0000
+++ b/read2mut.xml	Tue Feb 16 07:08:25 2021 +0000
@@ -20,6 +20,8 @@
         --trim '$trim'
         $chimera_correction
         --outputFile '$output_xlsx'
+        --outputFile2 '$output_xlsx2'
+        --outputFile3 '$output_xlsx3'
     ]]>
     </command>
     <inputs>
@@ -33,7 +35,9 @@
         <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/>
     </inputs>
     <outputs>
-        <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
+        <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
+        <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
+        <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
     </outputs>
     <tests>
         <test>
@@ -45,7 +49,9 @@
             <param name="phred" value="20"/>
             <param name="trim" value="10"/>
             <param name="chimera_correction" value="True"/>
-            <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/>
+            <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
+            <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
+            <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
         </test>
     </tests>
     <help> <![CDATA[
@@ -74,7 +80,7 @@
 
 **Output**
 
-The output is an XLSX file containing frequencies stats for DCS mutations based 
+The output are three XLSX files containing frequencies stats for DCS mutations based 
 on information from the raw reads. In addition to that a tier based 
 classification is provided based on the amout of support for a true variant call.