diff mut2read.xml @ 6:11a2a34f8a2b draft

planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/mut2read.xml	Tue Oct 27 12:46:55 2020 +0000
+++ b/mut2read.xml	Mon Jan 18 09:49:15 2021 +0000
@@ -1,10 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2read" name="DCS mutations to tags/reads:" version="1.0.1" profile="19.01">
+<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.0" profile="19.01">
     <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
     <macros>
         <import>va_macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+	<requirements>
+        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="1.4.0">matplotlib</requirement>
+        <requirement type="package" version="0.15">pysam</requirement>
+        <requirement type="package" version="0.11.6">cyvcf2</requirement>
+    </requirements>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
         ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
@@ -17,7 +22,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
+        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
         <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
         <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
     </inputs>
@@ -27,25 +32,25 @@
     </outputs>
     <tests>
         <test>
-            <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
-            <param name="file2" value="DCS_test_data_VA.bam"/>
-            <param name="file3" value="Aligned_Families_test_data_VA.tabular"/>
-            <output name="output_fastq" file="Interesting_Reads_test_data_VA.fastq" lines_diff="136"/>
-            <output name="output_json" file="tag_count_dict_test_data_VA.json" lines_diff="2"/>
+            <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/>
+            <param name="file2" value="DCS_test.bam"/>
+            <param name="file3" value="Aligned_Families_test.tabular"/>
+            <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/>
+            <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/>
         </test>
     </tests>
     <help> <![CDATA[
 **What it does**
 
-Takes a tabular file with mutations, a BAM file of aligned DCS reads, and a 
+Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a 
 tabular file with aligned families as input and prints all tags of reads that 
 carry a mutation to a user specified output file and creates a fastq file of 
 reads of tags with a mutation.
 
 **Input** 
 
-**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 
-generated by the **Variant Annotator** tool.
+**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
+generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
 
 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the 
 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.