# HG changeset patch
# User jowong
# Date 1542096221 18000
# Node ID 1bf76073c034ac2d1f230b70100e7f54bd41eb9c
# Parent  20c20bcdec36bb535eb48cc8489b14b30188e344
planemo upload

diff -r 20c20bcdec36 -r 1bf76073c034 spotyping.xml
--- a/spotyping.xml	Tue Nov 13 02:50:56 2018 -0500
+++ b/spotyping.xml	Tue Nov 13 03:03:41 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="spotyping" name="Spoligotype Prediction" version="0.1.5">
+<tool id="spotyping" name="Spoligotype Prediction" version="1.0.0">
     <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
     <requirements>
         <requirement type="package" version="2.1">spotyping</requirement>
@@ -28,7 +28,7 @@
                 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
             </when>
             <when value="single">
-                <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
+                <param name="input2" format="data" type="data_collection" label="input" help="Specify dataset with single reads"/>
             </when>
         </conditional>
         <section name="advanced" title="Advanced options" expanded="false">
@@ -44,7 +44,7 @@
         <data name="output3" label="query" format="excel.xls" from_work_dir="spotyping.xls"/>
     </outputs>
     <help><![CDATA[
-This is a modified version of IUC's wrapper of spotyping without the concatenation and renaming or input files. The wrapper also runs properly when supplied with paired-end reads
+This is a modified version of IUC's wrapper of spotyping without the concatenation and renaming of the input files. The wrapper also runs properly when supplied with paired-end reads
 
             SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
 
@@ -62,8 +62,6 @@
 
     **Options:**
 
-    \--noQuery
-    Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
 
     \--seq
     Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
@@ -71,17 +69,13 @@
     \-s SWIFT, --swift=SWIFT
     Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
 
-    \--sorted
-    Set if input reads are sorted relative to positions on a reference genome. If reads are sorted and swift mode is used, swift mode's sampling is adjusted
-    to sample reads across positions in the genome evenly.
+    \-m MIN, --min=MIN
+    minimum number of error-free hits to support presence of a spacer [Default: 5]
+    
+    \-r MIN_RELAX, --rmin=MIN_RELAX
+    minimum number of 1-error-tolerant hits to support presence of a spacer [Default: 6].
 
-    \--filter
-    Filter reads such that:
 
-    1. Leading and trailing 'N's would be removed.
-    2. Any read with more than 3 'N's in the middle would be removed.
-    3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given
-       the length of the flanking regions.
 
     **Got weird spoligotype prediction?**