diff mut2read.xml @ 0:e5953c54cfb5 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mut2read.xml	Sun Oct 04 17:19:39 2020 +0000
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="mut2read" name="DCS mutations to tags/reads:" version="1.0.1" 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"/>
+    <command><![CDATA[
+        ln -s '$file2' bam_input.bam &&
+        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
+        python '$__tool_directory__/mut2read.py' 
+        --mutFile '$file1'
+        --bamFile bam_input.bam
+        --familiesFile '$file3'
+        --outputFastq '$output_fastq' 
+        --outputJson '$output_json'
+    ]]>
+    </command>
+    <inputs>
+        <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
+        <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
+        <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
+    </inputs>
+    <outputs>
+        <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
+        <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
+    </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"/>
+        </test>
+    </tests>
+    <help> <![CDATA[
+**What it does**
+
+Takes a tabular 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 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>`_.
+
+**Dataset 3:** Tabular file with reads as produced by the 
+**Du Novo: Align families** tool of the `Du Novo Analysis Pipeline 
+<https://doi.org/10.1186/s13059-016-1039-4>`_
+
+**Output**
+
+The output is a json file containing dictonaries of the tags of reads containing mutations 
+in the DCS and a fastq file of all reads of these tags.
+
+    ]]> 
+    </help>
+    <expand macro="citation" />
+</tool>