# HG changeset patch
# User nml
# Date 1616184577 0
# Node ID 24a7a95867b088af3f44d13e130cd09836f46ce3
# Parent  17fcac7ddf546289ece07de590b0e23c0b02d06a
"planemo upload commit 683b11f79a83cf9e1563e46a75919157fa1136d4"

diff -r 17fcac7ddf54 -r 24a7a95867b0 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Mar 19 20:09:37 2021 +0000
@@ -0,0 +1,12 @@
+# SISTR - Salmonella In Silico Typing Resource (SISTR) commandline tool
+
+`SISTR` is a standalone serotyping module for *Salmonella* typing. The tool supports assembled genomes. 
+
+This Galaxy wrapper makes this tool accessible via Galaxy Project server and allows integration into workflows. Galaxy workflows include assembly and reporting steps for large sample sizes and are available to be installed from the main repository at <https://github.com/phac-nml/sistr_cmd>
+
+The tool can also be accessed via public instance at Galaxy EU at <https://usegalaxy.eu/root?tool_id=sistr_cmd>
+
+# Citation
+If you find this tool useful, please cite as
+
+><cite> The *Salmonella In Silico* Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft *Salmonella* genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101 </cite>
diff -r 17fcac7ddf54 -r 24a7a95867b0 sistr_cmd.xml
--- a/sistr_cmd.xml	Thu Aug 06 11:48:49 2020 -0400
+++ b/sistr_cmd.xml	Fri Mar 19 20:09:37 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@">
+<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@+galaxy1">
   <description>
     Salmonella In Silico Typing Resource commandline tool for serovar prediction 
   </description>
@@ -14,7 +14,7 @@
   <command><![CDATA[
   sistr 
     #for $fasta in $input_fastas
-      -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}'
+      -i '$fasta' '${$fasta.element_identifier.replace("." + $fasta.ext, "")}'
     #end for
     -f $output_format
     -o sistr-report.$output_format
@@ -39,7 +39,7 @@
       optional="false" 
       multiple="true"
       format="fasta"
-      />
+    />
     <param 
       name="output_format" 
       type="select"