# HG changeset patch
# User dcouvin
# Date 1629242842 0
# Node ID 1a7d6584e1ecc2a3a4253ebe361f1c555c0a911d
# Parent  f0e3646a4e459f6259e9c59277aedc5f6fa1541f
Uploaded

diff -r f0e3646a4e45 -r 1a7d6584e1ec MIRUReader.xml
--- a/MIRUReader.xml	Tue Aug 17 19:15:15 2021 +0000
+++ b/MIRUReader.xml	Tue Aug 17 23:27:22 2021 +0000
@@ -1,56 +1,55 @@
-<tool id="mirutool" name="mirureader" version="6.6.0">
-<description> MIRUReader.... </description>
+<tool id="mirureader" name="mirureader" version="1.0.0">
+<description> MIRUReader allows to perform in-silico MIRU-VNTR typing using long reads or assembled genome </description>
 
 <requirements>
-	<requirement type="package" version="3.2.0">python3-openid</requirement>
+<requirement type="package" version="3.2.0">python3-openid</requirement>
   <requirement type="package" version="6.6.0">emboss</requirement>
   <requirement type="package" version="1.3.2">pandas</requirement>
 </requirements>
 
-<command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p name 1> $output 2>$logfile</command>
-<!--
-     <command interpreter="bash" detect_errors="aggressive"><![CDATA[ 
+<!--<command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p sample 1> $output 2>$logfile</command>-->
+
+<command detect_errors="aggressive"><![CDATA[ 
 
 #import re
         ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
         ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
-        #set $named_input_files = ''
-        #for $input_file in $input_files
-            ## Add single quotes around each input file identifier
-            #set $_input_file = "'{}'".format($input_file.element_identifier)
-            ln -s '${input_file}' ${_input_file} && 
-            #set $named_input_files = $named_input_files + ' ' + $_input_file
-        #end for
+  
+        ## Add single quotes around each input file identifier
+        #set $_input_file = "'{}'".format($input.element_identifier)
+        #set $_input_file = $_input_file + '.fasta'
+        ln -s '${input}' ${_input_file} &&   
     
-        #for $element in $named_input_files
-            sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $element '-p' $element > $output
-        #end for
+        python3 $__tool_directory__/MIRUReader/MIRUReader.py -r $_input_file -p $_input_file > $output
+        
       
 
 
 ]]></command>
--->
 
 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output 
 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output  -->
 
 <inputs>
-	<!--
-	<param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
+<!--
+<param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
 -->
        <param format="fasta" name="input" type="data" label="Fasta file"/>
 </inputs>
 
 <outputs>
-	<data format="tabular" name="output" label="MIRUreader output"/>
-	<data format="txt" name="logfile" label="Logfile"/>
+<data format="tabular" name="output" label="MIRUReader output"/>
+<!--<data format="txt" name="logfile" label="LogFile"/>-->
 </outputs>
 
-<help>
--Git:https://github.com/phglab/MIRUReader.git
- </help>
+<help><![CDATA[
+MIRUReader allows to identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). It also work on assembled genome.
+
+GitHub: https://github.com/phglab/MIRUReader.git
+]]>
+</help>
 
 <citations>
-	<citation type="doi">10.1093/bioinformatics/btz771</citation>
+<citation type="doi">10.1093/bioinformatics/btz771</citation>
 </citations>
 </tool>