diff FunAnn/funct_annot.xml @ 0:1886293c2243 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FunAnn/funct_annot.xml	Thu Jul 23 12:49:09 2020 +0000
@@ -0,0 +1,31 @@
+<tool id="FunAnn" name="FunAnn" version="1">
+  <description> </description>
+  <requirements>
+    <requirement type="package" >perl</requirement>
+    <requirement type="package" >wget</requirement>
+    <requirement type="package" >gzip</requirement>
+  </requirements>
+  <command> <![CDATA[
+      ## ln -s $__tool_directory__/GCA_009858895.3_ASM985889v3_genomic.fna 2>>$log &&
+        cp $__tool_directory__/annotate.pl . 2>>$log &&
+	perl annotate.pl $infile $outfile 2>>$log
+          ]]>
+  </command>
+  <inputs>
+	<param name="infile" format="txt" type="data" label="merged show-snps tabular ouput" help="annotates SARS-CoV-2 variants" />
+  </inputs>
+  <outputs>
+	<data format="tsv" name="outfile" label="${tool.name} on ${on_string}: Functional annotation of SARS-CoV-2 genomes in tabular format " />
+	<data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
+  </outputs>
+  <help>
+	**What it does?**
+	
+This program reads a tabular formatted file, in pseudo vcf format, as obtained from the **join_nucmer** utility and performs functional annotation of SARS-CoV-2 variants. Please notice that the program performs minimum error checks, and that it is designed to work exclusively with the reference annotation of the SARS-CoV-2 genome as available from Genbank. A copy of the genome in fasta format can be found also in this Galaxy, under Shared Data -> Data Libraries -> SARS-CoV-2-REF. 
+
+
+The output file is again, a tabular file delineated by tabs, and providing different types of annotations for the variants included in the input file. A more detailed description of the output format can be found at : https://github.com/matteo14c/SARS-CoV-2_annot . 
+   </help>
+  <citations>
+  </citations>
+</tool>