# HG changeset patch
# User p.lucas
# Date 1644837304 0
# Node ID e93c20bad6b012135dbfd60c988126e6aa7d60a5

First upload wrapper

diff -r 000000000000 -r e93c20bad6b0 ClermonTyping_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ClermonTyping_wrapper.xml	Mon Feb 14 11:15:04 2022 +0000
@@ -0,0 +1,37 @@
+<tool id="ClermonTyping" name="ClermonTyping" version="1">
+  <description>
+    ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
+  </description>
+  <requirements>
+    <requirement type="package" version="1.79">biopython</requirement>
+    <requirement type="package" version="2.12.0">blast</requirement>
+    <requirement type="package" version="2.17.1.1">pandoc</requirement>
+    <requirement type="package" version="2.1.2">r-readr</requirement>
+    <requirement type="package" version="1.0.7">r-dplyr</requirement>
+    <requirement type="package" version="1.2.0">r-tidyr</requirement>
+    <requirement type="package" version="1.37">r-knitr</requirement>
+    <requirement type="package" version="1.4.0">r-stringr</requirement>
+    <requirement type="package" version="2.11">r-markdown</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse
+  ]]></command>
+  <inputs>
+    <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>
+  </inputs> 
+  <outputs>
+    <data name="html" format="html" label="html output file" from_work_dir="Analyse/Analyse.html"/>
+    <data name="phylogroup" format="tsv" label="Phylogroup found" from_work_dir="Analyse/Analyse_phylogroups.txt"/>
+  </outputs>
+  <help>
+    Script usage :
+      -h		: print this message and exit
+      -v		: print the version and exit
+      --fasta		: fasta contigs file(s). If multiple files, they must be separated by an arobase (@) value
+      --name		: name for this analysis (optional)
+      --threshold	: option for ClermontTyping, do not use contigs under this size (optional)
+      --minimal		: output a minimal set of files (optional)
+      --fastafile	: file with path of fasta contig file.  One file by line (optional)
+      --summary		: file with path of *_phylogroups.txt. One file by line (optional)
+  </help>
+</tool>