# HG changeset patch
# User dfornika
# Date 1512430565 18000
# Node ID d6619ce444f9c25fc8527a0cb8457074cdde3a4d
# Parent  25baf4a4b98edbb0b49526044b08f0cdb4cb722b
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7439570c55ac2a400c96d05135ab86d499fd612a-dirty

diff -r 25baf4a4b98e -r d6619ce444f9 data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml	Wed Oct 18 18:47:00 2017 -0400
+++ b/data_managers/data_manager_conf.xml	Mon Dec 04 18:36:05 2017 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.2">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.3">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -15,7 +15,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.2">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.3">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -30,7 +30,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.2">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.3">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
diff -r 25baf4a4b98e -r d6619ce444f9 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed Oct 18 18:47:00 2017 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Mon Dec 04 18:36:05 2017 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.2">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.3">
   <requirements>
-    <requirement type="package" version="0.1.2">mentalist</requirement>
+    <requirement type="package" version="0.1.3">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
diff -r 25baf4a4b98e -r d6619ce444f9 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Oct 18 18:47:00 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Mon Dec 04 18:36:05 2017 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.2">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.3">
   <requirements>
-    <requirement type="package" version="0.1.2">mentalist</requirement>
+    <requirement type="package" version="0.1.3">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r 25baf4a4b98e -r d6619ce444f9 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed Oct 18 18:47:00 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Mon Dec 04 18:36:05 2017 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.2">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.3">
   <requirements>
-    <requirement type="package" version="0.1.2">mentalist</requirement>
+    <requirement type="package" version="0.1.3">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r 25baf4a4b98e -r d6619ce444f9 tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Wed Oct 18 18:47:00 2017 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Mon Dec 04 18:36:05 2017 -0500
@@ -1,6 +1,6 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.2">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3">
   <requirements>
-    <requirement type="package" version="0.1.2">mentalist</requirement>
+    <requirement type="package" version="0.1.3">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     mentalist
@@ -10,17 +10,26 @@
     #if $discard_threshold
         -t '$discard_threshold'
     #end if
-    #if str( $fastq_input_selector ) == "single":
-        -s '$fastq_input1.name'
-        '$fastq_input1'
-    #else:
-        #if str( $fastq_input_selector ) == "paired":
-            -s '$fastq_input1.name'
-            '$fastq_input1' '$fastq_input2'
-	#end if	
+    #if $input_type.sPaired == "paired":
+       -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
+    #elif $input_type.sPaired == "collections":
+       -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
     #end if
   ]]></command>
   <inputs>
+    <conditional name="input_type">
+      <param name="sPaired" type="select" label="Single Pair or Collection">
+        <option value="collections">Paired-end Collections</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="paired">
+        <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
+        <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
+      </when>
+      <when value="collections">
+        <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
+      </when>
+    </conditional>
     <param name="kmer_db" type="select">
       <options from_data_table="mentalist_databases">
 	<validator type="no_options" message="No MentaLiST databases are available" />
@@ -32,20 +41,6 @@
     <param name="skip_length" type="integer"
 	   label="Skip Length" help="Skip length between consecutive k-mers."
 	   value="1" min="1" max="32" />
-    <conditional name="fastq_input">
-      <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
-	<option value="paired">Paired</option>
-	<option value="single">Single</option>
-	<option value="paired_collection">Paired Collection</option>
-      </param>
-      <when value="paired">
-	<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset with forward reads"/>
-	<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset with reverse reads"/>
-      </when>
-      <when value="single">
-	<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset with single reads"/>
-      </when>
-    </conditional>
   </inputs>
   <outputs>
     <data name="output_file" format="tabular"/>