diff profrep_masking.xml @ 0:a5f1638b73be draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/profrep_masking.xml	Wed Jun 26 08:01:42 2019 -0400
@@ -0,0 +1,27 @@
+<tool id="profrep_mask" name="ProfRep Masker" version="1.0.0">
+<description> Tool to mask repetitive regions of original DNA seq based on the repeat regions reported by ProfRep </description>
+<requirements>
+    <requirement type="package" version="1.0.0">profrep</requirement>
+</requirements>
+<command>
+python3 ${__tool_directory__}/profrep_masking.py --query ${input} --repeat_gff ${rp_gff} --mode ${mode} --output_masked ${out_masked}
+</command>
+<inputs>
+ <param format="fasta" type="data" name="input" label="Choose your input sequence to be masked" help="" />
+ <param format="gff" type="data" name="rp_gff" label="Choose GFF file of repetitive regions" help="" />
+ <param name="mode" type="select" label="Select the mode of masking" help="" >
+	 <option value="lowercase" selected="True">lowercase</option>
+     <option value="N">N</option>/>
+ </param>
+
+</inputs>
+
+<outputs>
+ <data format="fasta" name="out_masked" label="Masked DNA sequence(s) from dataset ${input.hid}" />
+</outputs>
+
+<help>
+**WHAT IT DOES**
+ This tool will mask repetitive regions of the original DNA sequence(s) based on repeats GFF. You can choose either lowercase(sequence will be preserved) or "N" mode of masking.
+</help>
+</tool>