--- a/prinseq.xml	Sat Jan 21 06:27:29 2017 -0500
+++ b/prinseq.xml	Fri Mar 03 14:58:49 2017 -0500
@@ -1,10 +1,6 @@
-<tool id="prinseq" name="PRINSEQ" version="0.1.0">
+<tool id="prinseq" name="PRINSEQ" version="0.20.4">
     <description>to process quality of sequences</description>
-    
     <requirements>
-        <requirement type="package" version="5.18.1">perl</requirement>
-        <!--<requirement type="package" version="2.90">perl-json</requirement>
-        <requirement type="package" version="1.106">perl-cairo</requirement>-->
         <requirement type="package" version="0.20.4">prinseq</requirement>
     </requirements>
 
@@ -34,13 +30,13 @@
 
         prinseq-lite.pl
             #if $seq_type.seq_type_opt == "single":
-                -fastq "$seq_type.input_singles"
+                -fastq '$seq_type.input_singles'
                 #if $seq_type.input_singles.is_of_type('fastqillumina'):
                     -phred64
                 #end if
             #else:
-                -fastq "$seq_type.input_mate1"
-                -fastq2 "$seq_type.input_mate2"
+                -fastq '$seq_type.input_mate1'
+                -fastq2 '$seq_type.input_mate2'
                 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
                     #import sys
                     #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
@@ -69,7 +65,7 @@
 
                 #set quality_filter_treatments=$filter_treatments.quality_filter_treatments
                 #if $quality_filter_treatments.apply_quality_filter_treatments == "true":
-                    #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments 
+                    #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
                     #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true":
                         -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
                     #end if
@@ -211,18 +207,17 @@
                     -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
                 #end if
 
-            #end if    
+            #end if
 
             #*
             -graph_stats "$graph_stats"
             -graph_data tmp/stats.gd
 
-        
-        && 
+        &&
 
         prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html
         *#
-]]> 
+]]>
     </command>
 
     <inputs>
@@ -261,7 +256,7 @@
                                 <param name="min_length_filter_treatment_value" type="integer" min="0" max="3000" value="60" label="Minimum length threshold to conserve sequences" help="(-min_len)"/>
                             </when>
                             <when value="false" />
-                        </conditional>  
+                        </conditional>
                         <conditional name="max_length_filter_treatments">
                             <param name="apply_max_length_filter_treatments" type="select" label="Filter too big sequences?" help="By default, no treatment based on a maximal length is made.">
                               <option value="true">Yes</option>
@@ -271,10 +266,10 @@
                                 <param name="max_length_filter_treatment_value" type="integer" min="0" max="3000" value="1000" label="Maximal length threshold to conserve sequences" help="(-max_len)"/>
                             </when>
                             <when value="false" />
-                        </conditional>  
+                        </conditional>
                     </when>
                     <when value="false" />
-                </conditional>  
+                </conditional>
                 <conditional name="quality_filter_treatments">
                     <param name="apply_quality_filter_treatments" type="select" label="Filter sequences based on quality score?" help="By default, sequences with a mean score below 15 are removed.">
                       <option value="true" selected="true">Yes</option>
@@ -312,7 +307,7 @@
                                       <option value="true" selected="true">Yes</option>
                                       <option value="false">No</option>
                                     </param>
-                                    <when value="true">   
+                                    <when value="true">
                                         <param name="min_mean_quality_filter_treatment_value" type="integer" min="0" max="40" value="15" label="Minimum mean score threshold to conserve sequences" help="(-min_qual_mean)"/>
                                     </when>
                                     <when value="false" />
@@ -322,7 +317,7 @@
                                       <option value="true">Yes</option>
                                       <option value="false" selected="true">No</option>
                                     </param>
-                                    <when value="true">   
+                                    <when value="true">
                                         <param name="max_mean_quality_filter_treatment_value" type="integer" min="0" max="40" value="40" label="Maximum mean score threshold to conserve sequences" help="(-max_qual_mean)"/>
                                     </when>
                                     <when value="false" />
@@ -401,14 +396,14 @@
                         <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help="(-lc_method)">
                             <option value="dust">Dust</option>
                             <option value="entropy" >Entropy</option>
-                        </param> 
+                        </param>
                         <param name="threshold_complexity_filter_treatments" type="integer" min="0" max="100" value="2" label="Threshold value used to filter sequences by sequence complexity" help="The dust method uses the threshold as maximum allowed score and the entropy method as minimum allowed value.(-lc_threshold)"/>
                     </when>
                     <when value="false" />
                 </conditional>
             </when>
             <when value="false" />
-        </conditional>  
+        </conditional>
 
         <conditional name="trimming_treatments">
             <param name="apply_trimming_treatments" type="select" label="Apply trimming treatments?" help="">
@@ -622,50 +617,41 @@
     </inputs>
 
     <outputs>
-        <data format="fastq" name="good_sequence_file" 
-            from_work_dir="tmp/good_sequences.fastq"
+        <data format="fastq" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
             label="${tool.name} on ${on_string}: Good sequences" >
             <filter>seq_type['seq_type_opt'] == "single"</filter>
         </data>
-        <data format="fastq" name="rejected_sequence_file" 
-            from_work_dir="tmp/rejected_sequences.fastq"
+        <data format="fastq" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences" >
             <filter>seq_type['seq_type_opt'] == "single"</filter>
         </data>
 
-        <data format="fastq" name="good_sequences_1_file" 
-            from_work_dir="tmp/good_sequences_1.fastq"
+        <data format="fastq" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
             label="${tool.name} on ${on_string}: Good sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="good_sequences_1_singletons_file" 
-            from_work_dir="tmp/good_sequences_1_singletons.fastq"
+        <data format="fastq" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
             label="${tool.name} on ${on_string}: Good singleton sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="rejected_sequence_1_file" 
-            from_work_dir="tmp/rejected_sequences_1.fastq"
+        <data format="fastq" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="good_sequences_2_file" 
-            from_work_dir="tmp/good_sequences_2.fastq"
+        <data format="fastq" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
             label="${tool.name} on ${on_string}: Good sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="good_sequences_2_singletons_file" 
-            from_work_dir="tmp/good_sequences_2_singletons.fastq"
+        <data format="fastq" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
             label="${tool.name} on ${on_string}: Good singleton sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="rejected_sequence_2_file" 
-            from_work_dir="tmp/rejected_sequences_2.fastq"
+        <data format="fastq" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
 
-        <!--<data format="html" name="html_file" 
-            from_work_dir="stats_html.html"
+        <!--<data format="html" name="html_file" from_work_dir="stats_html.html"
             label="${tool.name} on ${on_string}: Summary" />-->
     </outputs>
 
@@ -674,8 +660,8 @@
             <param name='seq_type_opt' value="single"/>
             <param name="input_singles" value="prinseq_input_sequences.fastq"/>
             <param name='apply_filter_treatments' value="true"/>
-            <param name='apply_length_filter_treatments' value="true"/> 
-            <param name='apply_min_length_filter_treatments' value="true"/>   
+            <param name='apply_length_filter_treatments' value="true"/>
+            <param name='apply_min_length_filter_treatments' value="true"/>
             <param name="min_length_filter_treatment_value" value="60"/>
             <param name='apply_max_length_filter_treatments' value="false" />
             <param name='apply_quality_filter_treatments' value="true"/>
@@ -688,7 +674,7 @@
             <param name='apply_base_content_filter_treatments' value="true"/>
             <param name='apply_GC_perc_content_filter_treatments' value="false"/>
             <param name='apply_N_number_content_filter_treatments' value="false"/>
-            <param name='apply_N_percentage_content_filter_treatments' value="true"/>  
+            <param name='apply_N_percentage_content_filter_treatments' value="true"/>
             <param name="N_percentage_content_filter_treatment_value" value="2"/>
             <param name='apply_other_base_content_filter_treatments' value="false"/>
             <param name='apply_complexity_filter_treatments' value="false"/>
@@ -710,11 +696,10 @@
     </tests>
 
     <help><![CDATA[
-
 **What it does**
 
 PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.
-This tool allow to process the sequences with filtering and trimming. 
+This tool allow to process the sequences with filtering and trimming.
 More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.
 
 -----
@@ -736,7 +721,7 @@
 
 Several filter treatments are proposed:
 
-  - Filters based on sequence length 
+  - Filters based on sequence length
   - Filters based on quality score
   - Filters based on base content
 
@@ -754,7 +739,6 @@
 
 The output file is a sequence file with sequences and quality from input file
 which have undergone filter and trimming.
-
     ]]>
     </help>