Mercurial > repos > p.lucas > get_iupac_percentage

changeset 1:2dc9d2efce29 draft

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Uploaded wrapper
author p.lucas
date Tue, 11 Jun 2024 09:42:49 +0000
parents 21e3c46d9656
children 014e2d31e596
files FA_IUPAC_count.xml
diffstat 1 files changed, 29 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FA_IUPAC_count.xml	Tue Jun 11 09:42:49 2024 +0000
@@ -0,0 +1,29 @@
+<tool id="get_iupac" name="Count IUPAC bases" version="1">
+  <description>
+    From fasta fail, count IUPAC bases.
+  </description>
+  <requirements>
+    <requirement type="package" version="1.79">biopython</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command interpreter="python" detect_errors="exit_code"><![CDATA[
+    FA_IUPAC_count.py 
+      -i "$reference_fasta" 
+      -o "$output_iupac" 
+  ]]></command>
+  <inputs>
+    <param name="reference_fasta" type="data" format="fasta" label="Fasta file" help="Fasta file to count IUPAC"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output_iupac" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <help>
+  <![CDATA[
+
+Homemade script to count all IUPAC bases in sequences and get percentage of IUPAC in each sequence.
+
+  ]]>
+  </help>
+</tool>