# HG changeset patch
# User iuc
# Date 1536331836 14400
# Node ID 56591ec04525a2814e8453b85f777f2ab5615f87
# Parent  3f163b178c5ca67778665d0e76e7947156e21493
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7

diff -r 3f163b178c5c -r 56591ec04525 art_solid.xml
--- a/art_solid.xml	Tue Jun 28 11:32:06 2016 -0400
+++ b/art_solid.xml	Fri Sep 07 10:50:36 2018 -0400
@@ -8,51 +8,52 @@
   <command><![CDATA[
 art_SOLiD
 
-$sam
+    $sam
 
-#if $rndSeed and $rndSeed > -1:
-    -r $rndSeed
-#end if
+    #if $rndSeed and $rndSeed > -1:
+        -r $rndSeed
+    #end if
+
+    #if $generate.amplicon.use_amplicon == "amplicon_true":
+        -A
 
-#if $generate.amplicon.use_amplicon == "amplicon_true":
-    -A
+        #if $generate.choice == "single_end":
+            s
+        #else if $generate.choice == "paired_end":
+            p
+        #else:
+            m
+        #end if
 
-    #if $generate.choice == "single_end":
-    s
-    #else if $generate.choice == "paired_end":
-    p
-    #else:
-    m
     #end if
 
-#end if
-
-$input_seq_file
-output
+    '$input_seq_file'
+    output
 
-#if $generate.choice == "single_end":
-    $generate.LEN_READ
-    $fold_coverage
-#else if $generate.choice == "paired_end":
-    $generate.LEN_READ_F3
-    $generate.LEN_READ_F5
-    $fold_coverage
-    $generate.fragment_size
-    $generate.fragment_sd
-#else:
-    $generate.LEN_READ
-    $fold_coverage
-    $generate.fragment_size
-    $generate.fragment_sd
-#end if
+    #if $generate.choice == "single_end":
+        $generate.LEN_READ
+        $fold_coverage
+    #else if $generate.choice == "paired_end":
+        $generate.LEN_READ_F3
+        $generate.LEN_READ_F5
+        $fold_coverage
+        $generate.fragment_size
+        $generate.fragment_sd
+    #else:
+        $generate.LEN_READ
+        $fold_coverage
+        $generate.fragment_size
+        $generate.fragment_sd
+    #end if
 
-#if $generate.amplicon.use_amplicon == "amplicon_true":
-    #if $generate.choice == "single_end":
-        $generate.amplicon.reads_per_amplicon
-    #else:
-        $generate.amplicon.read_pairs_per_amplicon
+    #if $generate.amplicon.use_amplicon == "amplicon_true":
+        #if $generate.choice == "single_end":
+            $generate.amplicon.reads_per_amplicon
+        #else:
+            $generate.amplicon.read_pairs_per_amplicon
+        #end if
     #end if
-#end if
+
 ]]></command>
   <inputs>
     <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
diff -r 3f163b178c5c -r 56591ec04525 macros.xml
--- a/macros.xml	Tue Jun 28 11:32:06 2016 -0400
+++ b/macros.xml	Fri Sep 07 10:50:36 2018 -0400
@@ -63,7 +63,7 @@
 
     <xml name="frag_len_sd">
         <param label="the average DNA fragment size"
-            name="fragment_size" type="integer" value="200" minimum="101" />
+            name="fragment_size" type="integer" value="200" />
         <param label="the standard deviation of the DNA fragment size"
             name="fragment_sd" type="integer" value="0"/>
     </xml>
diff -r 3f163b178c5c -r 56591ec04525 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 28 11:32:06 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="art" version="2014_11_03">
-    <repository changeset_revision="10c1f6e14834" name="package_art_2014_11_03" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>