changeset 42:da224c392a54 draft

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

--- a/read2mut.py	Wed Feb 24 13:14:28 2021 +0000
+++ b/read2mut.py	Wed Feb 24 14:20:17 2021 +0000
@@ -60,9 +60,9 @@
     parser.add_argument('--phred', type=int, default=20,
                         help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.')
     parser.add_argument('--trim5', type=int, default=10,
-                        help='Integer threshold for assigning mutations at start of reads to lower tier. Default 10.')
+                        help='Integer threshold for assigning mutations at the beginning of the reads to lower tier. Default 10.')
     parser.add_argument('--trim3', type=int, default=10,
-                        help='Integer threshold for assigning mutations at end of reads to lower tier. Default 10.')
+                        help='Integer threshold for assigning mutations at the end of the reads to lower tier. Default 10.')
     parser.add_argument('--chimera_correction', action="store_true",
                         help='Count chimeric variants and correct the variant frequencies')
     return parser

--- a/read2mut.xml	Wed Feb 24 13:14:28 2021 +0000
+++ b/read2mut.xml	Wed Feb 24 14:20:17 2021 +0000
@@ -33,8 +33,8 @@
         <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
         <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
         <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
-        <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/>
-        <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at the end of reads to lower tier. Default 10."/>
+        <param name="trim5" type="integer" label="Trimming threshold at 5' end of reads" value="10" help="Integer threshold for assigning mutations at the beginning of reads to a lower tier. Default 10."/>
+        <param name="trim3" type="integer" label="Trimming threshold at 3' end of reads" value="10" help="Integer threshold for assigning mutations at the end of reads to a lower tier. Default 10."/>
         <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>
@@ -53,7 +53,6 @@
             <param name="phred" value="20"/>
             <param name="trim5" value="10"/>
             <param name="trim3" value="10"/>
-            <param name="delim_csv" value=","/>
             <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
             <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
             <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
@@ -71,7 +70,7 @@
 **Input** 
 
 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
-generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
+generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
 
 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the 
 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
@@ -87,7 +86,7 @@
 **Output**
 
 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 
+on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that a tier based 
 classification is provided based on the amout of support for a true variant call.
 
     ]]>