# HG changeset patch
# User mheinzl
# Date 1616162739 0
# Node ID 3691922baa088dd9a4abb544cc9da178dfb1383d
# Parent  8664c0aa91c362657b41431edb628c22476b94b4
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r 8664c0aa91c3 -r 3691922baa08 mut2read.xml
--- a/mut2read.xml	Fri Mar 19 13:54:14 2021 +0000
+++ b/mut2read.xml	Fri Mar 19 14:05:39 2021 +0000
@@ -1,15 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" profile="19.01">
+<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.1.0" 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>
-	<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>
+    <expand macro="requirements"/>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
         ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
@@ -50,7 +45,8 @@
 **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 DCS reads. This file can be obtained by the 
 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
diff -r 8664c0aa91c3 -r 3691922baa08 mut2sscs.xml
--- a/mut2sscs.xml	Fri Mar 19 13:54:14 2021 +0000
+++ b/mut2sscs.xml	Fri Mar 19 14:05:39 2021 +0000
@@ -1,15 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.1" profile="19.01">
+<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.1.0" profile="19.01">
     <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description>
     <macros>
         <import>va_macros.xml</import>
     </macros>
-    <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>
+    <expand macro="requirements"/>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
         ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
@@ -43,7 +38,7 @@
 **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 single stranded consensus sequence (SSCS) 
 reads. This file can be obtained by the tool `Map with BWA-MEM 
diff -r 8664c0aa91c3 -r 3691922baa08 read2mut.xml
--- a/read2mut.xml	Fri Mar 19 13:54:14 2021 +0000
+++ b/read2mut.xml	Fri Mar 19 14:05:39 2021 +0000
@@ -1,15 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="2.1.2" profile="17.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="2.1.2" profile="19.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
     </macros>
-    <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>
+    <expand macro="requirements">
         <requirement type="package" version="1.1.0">xlsxwriter</requirement>
-        <requirement type="package" version="0.11.6">cyvcf2</requirement>
+    </expand>
     </requirements>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
diff -r 8664c0aa91c3 -r 3691922baa08 va_macros.xml
--- a/va_macros.xml	Fri Mar 19 13:54:14 2021 +0000
+++ b/va_macros.xml	Fri Mar 19 14:05:39 2021 +0000
@@ -1,20 +1,28 @@
 <macros>
     <xml name="citation">
-    <citations>
-        <citation type="bibtex">
-            @article{duplex,
-            author = {Povysil, Gundula and Heinzl, Monika and Salazar, Renato and Stoler, Nicholas and Nekrutenko, Anton and Tiemann-Boege, Irene},
-            doi = {10.1093/nargab/lqab002},
-            issn = {2631-9268},
-            number = {1},
-            journal = {NAR Genomics and Bioinformatics},
-            publisher = {NAR Genomics and Bioinformatics},
-            title = {{Increased yields of duplex sequencing data by a series of quality control tools}}
-            url = {https://pubmed.ncbi.nlm.nih.gov/33575654},
-            volume = {3},
-            year = {2021}
-         }
-        </citation>
-    </citations>
-</xml>
+        <citations>
+            <citation type="bibtex">
+                @misc{duplex,
+                author = {Povysil, Gundula and Heinzl, Monika and Salazar, Renato and Stoler, Nicholas and Nekrutenko, Anton and Tiemann-Boege, Irene},
+                doi = {10.1093/nargab/lqab002},
+                issn = {2631-9268},
+                number = {1},
+                journal = {NAR Genomics and Bioinformatics},
+                publisher = {NAR Genomics and Bioinformatics},
+                title = {{Increased yields of duplex sequencing data by a series of quality control tools}}
+                url = {https://pubmed.ncbi.nlm.nih.gov/33575654},
+                volume = {3},
+                year = {2021}
+             }
+            </citation>
+        </citations>
+    </xml>
+    <xml name="requirements">
+         <requirements>
+             <requirement type="package" version="3.1.2">matplotlib</requirement>
+             <requirement type="package" version="0.15">pysam</requirement>
+             <requirement type="package" version="0.11.6">cyvcf2</requirement>
+             <yield/>
+         </requirements>
+    </xml>
 </macros>
\ No newline at end of file