# HG changeset patch
# User bebatut
# Date 1453884909 18000
# Node ID acaf871de2ea5b92aeac19e634ab244e38e077f1
# Parent  10ac5c567b7355b57a02919c963bfe200d727176
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty

diff -r 10ac5c567b73 -r acaf871de2ea README.md
--- a/README.md	Tue Nov 17 06:02:09 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-Galaxy wrapper for PRINSEQ
-===========================
-
-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. For more information, check the 
-[user manual](http://prinseq.sourceforge.net/manual.html)
-
-# Installation
-
-## Automated installation
-
-On a Galaxy instance, the wrapper can be automatically installed using the 
-ToolShed. This will automatically install the dependencies, configure the Galaxy
-instance for the tool and data, ...
-
-## Manual installation
-
-For manual installation, the files `prinseq.xml` must be put in the `tools/prinseq/`
- folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as 
-normal:
-
-```
-<section name="Control quality" id="prinseq">
-    <tool file="prinseq/prinseq.xml" />
-</section>
-```
-
-PRINSEQ must be installed somewhere on the system path. It can be done using:
-
-```
-planemo dependency_script ~/repositories/galaxytools/tools/prinseq/
-bash dep_install.sh
-source env.sh
-```
-
-To test the Galaxy integration, the functional tests can be runned:
-
-```
-./run_tests.sh -sid prinseq
-```
-
-# Bug Reports
-
-Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
-
-# Developers
-
-A release can be pushed to the test or main "Galaxy Tool Shed", using the following 
-Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
-
-```
-planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/prinseq/
-```
-
-or:
-
-```
-planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/prinseq/
-```
-
-# License (Apache 2) 
-
-This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details
\ No newline at end of file
diff -r 10ac5c567b73 -r acaf871de2ea prinseq.xml
--- a/prinseq.xml	Tue Nov 17 06:02:09 2015 -0500
+++ b/prinseq.xml	Wed Jan 27 03:55:09 2016 -0500
@@ -25,8 +25,24 @@
 
     <command>
 <![CDATA[
-        perl \${PRINSEQ_DIR}/prinseq-lite.pl    
-            -fastq $sequence_to_control_file
+        perl \${PRINSEQ_DIR}/prinseq-lite.pl
+            #if $seq_type.seq_type_opt == 'single':
+                -fastq "$seq_type.input_singles"
+                #if $seq_type.input_singles.ext == 'fastqillumina':
+                    -phred64
+                #end if
+            #else:
+                -fastq "$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.' )
+                #end if
+                #if $seq_type.input_mate1.ext == 'fastqillumina':
+                    -phred64
+                #end if
+            #end if
+
             -out_good good_sequences
             -out_bad rejected_sequences
 
@@ -37,6 +53,7 @@
                     #if $min_length_filter_treatments.apply_min_length_filter_treatments :
                         -min_len $min_length_filter_treatments.min_length_filter_treatment_value
                     #end if
+
                     #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments
                     #if $max_length_filter_treatments.apply_max_length_filter_treatments :
                         -max_len $max_length_filter_treatments.max_length_filter_treatment_value
@@ -49,16 +66,19 @@
                     #if $min_quality_filter_treatments.apply_min_quality_filter_treatments :
                         -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
                     #end if
+
                     #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments
                     #if $max_quality_filter_treatments.apply_max_quality_filter_treatments :
                         -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
                     #end if
+
                     #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments
                     #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments:
                         #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments
                         #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments:
                             -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
                         #end if
+
                         #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments
                         #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments:
                             -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
@@ -74,22 +94,24 @@
                         #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments :
                             -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
                         #end if
-                        set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
+
+                        #set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
                         #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments :
                             -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
                         #end if
                     #end if
+
                     #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments
                     #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments :
                         -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
                     #end if
+
                     #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments
                     #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments :
                         -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value
                     #end if
-                    #if $base_content_filter_treatments.apply_other_base_content_filter_treatments :
-                        -noniupac
-                    #end if
+
+                    $base_content_filter_treatments.apply_other_base_content_filter_treatments
                 #end if
 
                 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments
@@ -114,17 +136,20 @@
                         #if $left_position_trimming_treatments.apply_left_position_trimming_treatments :
                             -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
                         #end if
+
                         #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments
                         #if $right_position_trimming_treatments.apply_right_position_trimming_treatments :
                             -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
                         #end if
                     #end if
+
                     #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments
                     #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments :
                         #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments
                         #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments :
                             -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
                         #end if
+
                         #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments
                         #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments :
                             -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
@@ -140,17 +165,20 @@
                         #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments :
                             -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
                         #end if
+
                         #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
-                        #if right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments :
+                        #if $right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments :
                             -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
                         #end if
                     #end if
+
                     #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments
                     #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments :
                         #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments
                         #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments :
                             -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
                         #end if
+
                         #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments
                         #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments :
                             -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
@@ -164,96 +192,130 @@
                     #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments :
                         -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
                     #end if
+
                     #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments
                     #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments :
                         -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value
                     #end if
+
                     -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments
                     -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments
                     -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments
                     -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
                 #end if
 
-            #end if
-]]>
+            #end if    
+
+            -graph_stats "$graph_stats"
+            -graph_data stats.gd
+        ;
+
+        # perl \${PRINSEQ_DIR}/prinseq-graphs-noPCA.pl -i stats.gd -html_all -o stats_html
+
+        
+]]> 
     </command>
 
     <inputs>
-        <param name="sequence_to_control_file" type="data" format="fastq" label="Input 
-            sequence file" help="The file must be in fastq format for quality 
-            scores"/>
+        <conditional name="seq_type">
+            <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
+            </when>
+            <when value="paired">
+                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
+                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
+            </when>
+        </conditional>
 
         <conditional name="filter_treatments">
             <param name='apply_filter_treatments' type='boolean' checked="true" 
-                label="Apply filter treatments?" help=""/>
+                truevalue="true" falsevalue="false" label="Apply filter treatments?" 
+                help=""/>
             <when value="true">
                 <conditional name="length_filter_treatments">
                     <param name='apply_length_filter_treatments' type='boolean' 
-                        checked="true" label="Filter sequence based on their 
-                        length?" help="By default, sequences smaller than 60 bp 
+                        checked="true" truevalue="true" falsevalue="false" 
+                        label="Filter sequence based on their length?" help="By 
+                        default, sequences smaller than 60 bp 
                         are removed. No top threshold is defined"/> 
                     <when value="true">
                         <conditional name="min_length_filter_treatments">
                             <param name='apply_min_length_filter_treatments' 
-                                type='boolean' checked="true" label="Filter too 
+                                type='boolean' checked="true" truevalue="true" 
+                                falsevalue="false" label="Filter too 
                                 small sequences?" help="By default, sequences 
                                 smaller than 60 bp are removed."/>   
                             <when value="true">
                                 <param name="min_length_filter_treatment_value" type="integer" min="0" 
                                     max="3000" value="60" label="Minimum length t
-                                    hreshold to conserve sequences" help=""/>
+                                    hreshold to conserve sequences" help="(-min_len)"/>
                             </when>
+                            <when value="false" />
                         </conditional>  
                         <conditional name="max_length_filter_treatments">
                             <param name='apply_max_length_filter_treatments' 
-                                type='boolean' checked="false" label="Filter too 
+                                type='boolean' truevalue="true" falsevalue="false" 
+                                checked="false" label="Filter too 
                                 big sequences?" help="By default, no treatment 
                                 based on a maximal length is made"/>
                             <when value="true">
                                 <param name="max_length_filter_treatment_value" type="integer" min="0" 
                                     max="3000" value="1000" label="Maximal length 
-                                    threshold to conserve sequences" help=""/>
+                                    threshold to conserve sequences" help="(-max_len)"/>
                             </when>
+                            <when value="false" />
                         </conditional>  
                     </when>
+                    <when value="false" />
                 </conditional>  
                 <conditional name="quality_filter_treatments">
                     <param name='apply_quality_filter_treatments' type='boolean' 
-                        checked="true" label="Filter sequences based on quality 
+                        checked="true" truevalue="true" falsevalue="false"
+                        label="Filter sequences based on quality 
                         score?" help="By default, sequences with a mean score 
                         below 15 are removed."/>
                     <when value="true">
                         <conditional name="min_quality_filter_treatments">
                             <param name='apply_min_quality_filter_treatments' 
-                                type='boolean' checked="false" label="Filter sequences 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Filter sequences 
                                 based on their minimum score?" help="By default, 
                                 no treatment based on a minimum score is made"/>
                             <when value="true">
                                 <param name="min_quality_filter_treatment_value" type="integer" min="0" 
                                     max="40" value="2" label="Minimum score threshold 
-                                    to conserve sequences" help=""/>
+                                    to conserve sequences" help="(-min_qual_score)"/>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="max_quality_filter_treatments">
                             <param name='apply_max_quality_filter_treatments' 
-                                type='boolean' checked="false" label="Filter sequences 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Filter sequences 
                                 based on their maximum score?" help="By default, 
                                 no treatment based on a maximum score is made"/>
                             <when value="true">
                                 <param name="max_quality_filter_treatment_value" type="integer" min="0" 
                                     max="40" value="38" label="Maximum score 
-                                    threshold to conserve sequences" help=""/>
+                                    threshold to conserve sequences" help="(-max_qual_score)"/>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="mean_quality_filter_treatments">
                             <param name='apply_mean_quality_filter_treatments' 
-                                type='boolean' checked="true" label="Filter sequences 
+                                type='boolean' checked="true" truevalue="true" 
+                                falsevalue="false" label="Filter sequences 
                                 based on their mean score?" help="By default, 
                                 sequences with a mean score below 15 are removed."/>
                             <when value="true">
                                 <conditional name="min_mean_quality_filter_treatments">
                                     <param name='apply_min_mean_quality_filter_treatments' 
-                                        type='boolean' checked="true" label="Filter 
+                                        type='boolean' checked="true" truevalue="true" 
+                                        falsevalue="false" label="Filter 
                                         sequences with too small mean score?" 
                                         help="By default, sequences with a mean 
                                         score below 15 are removed."/>
@@ -262,12 +324,14 @@
                                             type="integer" min="0" 
                                             max="40" value="15" label="Minimum mean 
                                             score threshold to conserve sequences" 
-                                            help=""/>
+                                            help="(-min_qual_mean)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                                 <conditional name="max_mean_quality_filter_treatments">
                                     <param name='apply_max_mean_quality_filter_treatments' 
-                                        type='boolean' checked="false" label="Filter 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Filter 
                                         sequences with too high mean score?" 
                                         help="By default, no treatment based on 
                                         a maximum mean score is made"/>
@@ -276,29 +340,35 @@
                                             type="integer" 
                                             min="0" max="40" value="40" 
                                             label="Maximum mean score threshold 
-                                            to conserve sequences" help=""/>
+                                            to conserve sequences" help="(-max_qual_mean)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                             </when>
+                            <when value="false" />
                         </conditional>
                     </when>
+                    <when value="false" />
                 </conditional>
                 <conditional name="base_content_filter_treatments">
                     <param name='apply_base_content_filter_treatments' 
-                        type='boolean' checked="true" label="Filter sequences 
-                        based on their base content?" help="By default, sequences 
+                        type='boolean' checked="true" truevalue="true" falsevalue="false" 
+                        label="Filter sequences based on their base content?" 
+                        help="By default, sequences 
                         with more than 2% of N bases are removed."/>
                     <when value="true">
                         <conditional name="GC_perc_content_filter_treatments">
                             <param name='apply_GC_perc_content_filter_treatments' 
-                                type='boolean' checked="false" label="Filter 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Filter 
                                 sequences based on their GC percentage?" 
                                 help="By default, no treatment based on GC percentage 
                                 is made."/>
                             <when value="true">
                                 <conditional name="min_GC_perc_content_filter_treatments">
                                     <param name='apply_min_GC_perc_content_filter_treatments' 
-                                        type='boolean' checked="false" label="Filter 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Filter 
                                         sequences with too small GC percentage?" 
                                         help="By default, no treatment based on 
                                         GC percentage is made."/>
@@ -307,12 +377,14 @@
                                             type="integer" min="0" 
                                             max="100" value="10" label="Minimal 
                                             GC percentage threshold to conserve 
-                                            sequences" help=""/>
+                                            sequences" help="(-min_gc)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                                 <conditional name="max_GC_perc_content_filter_treatments">
                                     <param name='apply_max_GC_perc_content_filter_treatments' 
-                                        type='boolean' checked="false" label="Filter 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Filter 
                                         sequences with too high GC percentage?" 
                                         help="By default, no treatment based on 
                                         GC percentage is made."/>
@@ -321,27 +393,32 @@
                                             type="integer" min="0" 
                                             max="100" value="90" label="Maximal GC
                                              percentage threshold to conserve 
-                                             sequences" help=""/>
+                                             sequences" help="(-max_gc)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="N_number_content_filter_treatments">
                             <param name='apply_N_number_content_filter_treatments' 
-                                type='boolean' checked="false" label="Filter 
-                                sequences based on their number of N bases?" 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Filter sequences based 
+                                on their number of N bases?" 
                                 help="By default, no treatment based on N number 
                                 is made."/>
                             <when value="true">
                                 <param name="N_number_content_filter_treatment_value" 
                                     type="integer" min="0" 
                                     max="3000" value="10" label="Maximal N number 
-                                    threshold to conserve sequences" help=""/>
+                                    threshold to conserve sequences" help="(-ns_max_n)"/>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="N_percentage_content_filter_treatments">
                             <param name='apply_N_percentage_content_filter_treatments' 
-                                type='boolean' checked="true" label="Filter sequences 
+                                type='boolean' checked="true" truevalue="true" 
+                                falsevalue="false" label="Filter sequences 
                                 based on their percentage of N bases?" help="By 
                                 default, sequences with more than 2% of N bases 
                                 are removed."/>  
@@ -349,24 +426,28 @@
                                 <param name="N_percentage_content_filter_treatment_value"
                                      type="integer" min="0" max="100" 
                                     value="2" label="Maximal N percentage threshold 
-                                    to conserve sequences" help=""/>
+                                    to conserve sequences" help="(-ns_max_p)"/>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <param name='apply_other_base_content_filter_treatments' 
-                            type='boolean' checked="false" label="Filter sequences 
+                            type='boolean' truevalue="-noniupac" falsevalue=""
+                            checked="false" label="Filter sequences 
                             with characters other than A, T, C, G and N?" help="By 
-                            default, this treatment is not made."/>
+                            default, this treatment is not made. (-noniupac)"/>
                     </when>
+                    <when value="false" />
                 </conditional>
                 <conditional name="complexity_filter_treatments">
                     <param name='apply_complexity_filter_treatments' type='boolean' 
-                        checked="false" label="Filter sequences based on their 
+                        checked="false" truevalue="true" falsevalue="false"
+                        label="Filter sequences based on their 
                         complexity?" help="By default, no complexity filter is 
                         applied"/>
                     <when value="true">
                         <param name="method_complexity_filter_treatments" type="select" 
                             display="radio" label="Method to filter low complexity 
-                            sequences" help="">
+                            sequences" help="(-lc_method)">
                             <option value="dust">Dust</option>
                             <option value="entropy" >Entropy</option>
                         </param> 
@@ -374,29 +455,35 @@
                             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."/>
+                            and the entropy method as minimum allowed value.(-lc_threshold)"/>
                     </when>
+                    <when value="false" />
                 </conditional>
             </when>
+            <when value="false" />
         </conditional>  
 
         <conditional name="trimming_treatments">
             <param name='apply_trimming_treatments' type='boolean' checked="true" 
-                label="Apply trimming treatments?" help=""/>
+                truevalue="true" falsevalue="false" label="Apply trimming 
+                treatments?" help=""/>
             <when value="true">
                 <conditional name="length_trimming_treatments">
                     <param name='apply_length_trimming_treatments' type='boolean' 
-                        checked="false" label="Trim all sequences from the 3'-end 
+                        checked="false" truevalue="true" falsevalue="false" 
+                        label="Trim all sequences from the 3'-end 
                         to a length?" help="By default, no length trimming is made"/>
                     <when value="true">
                         <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" 
                             value="100" label="Length of sequences after 
-                            trimming" help=""/>
+                            trimming" help="(-trim_to_len)"/>
                     </when>
+                    <when value="false" />
                 </conditional>
                 <conditional name="position_trimming_treatments">
                     <param name='apply_position_trimming_treatments' type='boolean' 
-                        checked="false" label="Trim all sequences from the ends?" 
+                        checked="false" truevalue="true" falsevalue="false" 
+                        label="Trim all sequences from the ends?" 
                         help="By default, no position trimming is made"/>
                     <when value="true">
                         <conditional name="nb_position_trimming_treatments">
@@ -407,7 +494,8 @@
                             <when value="true">
                                 <conditional name="left_position_trimming_treatments">
                                     <param name='apply_left_position_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim 
                                         sequences at the 5'-end by a defined number 
                                         of positions?" help="By default, no position 
                                         trimming is made"/>
@@ -415,12 +503,14 @@
                                         <param name="left_position_trimming_treatment_value" 
                                             type="integer" min="0" 
                                             max="3000" value="100" label="Number of 
-                                            positions to trim on 5'-end" help=""/>
+                                            positions to trim on 5'-end" help="(-trim_left)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                                 <conditional name="right_position_trimming_treatments">
                                     <param name='apply_right_position_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim 
                                         sequences at the 3'-end by a defined number 
                                         of positions?" help="By default, no position 
                                         trimming is made"/>
@@ -429,22 +519,26 @@
                                             type="integer" min="0" 
                                             max="3000" value="100" label="Number 
                                             of positions to trim on 3'-end" 
-                                            help=""/>
+                                            help="(-trim_right)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="percentage_position_trimming_treatments">
                             <param name='apply_percentage_position_trimming_treatments' 
-                                type='boolean' checked="false" label="Trim sequences 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Trim sequences 
                                 by a defined percentage of read length?" help="By 
                                 default, no position trimming is made. The trim 
                                 length is rounded towards the lower integer"/>
                             <when value="true">
                                 <conditional name="left_percentage_position_trimming_treatments">
                                     <param name='apply_left_percentage_position_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
-                                        sequences at the 5'-end by a defined percentage 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim sequences 
+                                        at the 5'-end by a defined percentage 
                                         of read length?" help="By default, no position 
                                         trimming is made. The trim length is rounded 
                                         towards the lower integer"/>
@@ -452,12 +546,14 @@
                                         <param name="left_percentage_position_trimming_treatment_value" 
                                             type="integer" min="0" 
                                             max="100" value="2" label="Percentage 
-                                            of positions to trim on 5'-end" help=""/>
+                                            of positions to trim on 5'-end" help="(-trim_left_p)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                                 <conditional name="right_percentage_position_trimming_treatments">
                                     <param name='apply_right_percentage_position_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim 
                                         sequences at the 3'-end by a defined percentage 
                                         of read length?" help="By default, no position 
                                         trimming is made. The trim length is rounded 
@@ -466,27 +562,33 @@
                                         <param name="right_percentage_position_trimming_treatment_value" 
                                             type="integer" min="0" 
                                             max="100" value="2" label="Percentage 
-                                            of positions to trim on 3'-end" help=""/>
+                                            of positions to trim on 3'-end" help="(-trim_right_p)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                             </when>
+                            <when value="false" />
                         </conditional>
                     </when>
+                    <when value="false" />
                 </conditional>
                 <conditional name="tail_trimming_treatments">
                     <param name='apply_tail_trimming_treatments' type='boolean' 
-                        checked="false" label="Trim tails?" help="By default, no 
+                        checked="false" truevalue="true" falsevalue="false" 
+                        label="Trim tails?" help="By default, no 
                         tail trimming is made"/>
                     <when value="true">
                         <conditional name="a_t_tail_trimming_treatments">
                             <param name='apply_a_t_tail_trimming_treatments' 
-                                type='boolean' checked="false" label="Trim poly-A/T 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Trim poly-A/T 
                                 tail?" help="By default, no poly-A/T tail trimming 
                                 is made"/>
                             <when value="true">
                                 <conditional name="left_a_t_tail_trimming_treatments">
                                     <param name='apply_left_a_t_tail_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim 
                                         poly-A/T tail at the 5'-end?" help="By 
                                         default, no 5'-end poly-A/T tail trimming 
                                         is made"/>
@@ -495,12 +597,14 @@
                                             type="integer" min="0" 
                                             max="3000" value="100" label="Minimum 
                                             length of poly-A/T to trim at the 5'-end" 
-                                            help=""/>
+                                            help="(-trim_tail_left)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                                 <conditional name="right_a_t_tail_trimming_treatments">
                                     <param name='apply_right_a_t_tail_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim poly-A/T 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim poly-A/T 
                                         tail at the 5'-end?" help="By default, no 
                                         3'-end poly-A/T tail trimming is made"/>
                                     <when value="true">
@@ -508,19 +612,23 @@
                                              type="integer" min="0" 
                                             max="3000" value="100" label="Minimum 
                                             length of poly-A/T to trim at the 5'-end" 
-                                            help=""/>
+                                            help="(-trim_tail_right)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="ns_tail_trimming_treatments">
                             <param name='apply_ns_tail_trimming_treatments' type='boolean' 
-                                checked="false" label="Trim poly-N tail?" help="By 
+                                checked="false" truevalue="true" falsevalue="false" 
+                                label="Trim poly-N tail?" help="By 
                                 default, no poly-N tail trimming is made"/>
                             <when value="true">
                                 <conditional name="left_ns_tail_trimming_treatments">
                                     <param name='apply_left_ns_tail_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim 
                                         poly-N tail at the 5'-end?" help="By default, 
                                         no 5'-end poly-N tail trimming is made"/>
                                     <when value="true">
@@ -528,12 +636,14 @@
                                             type="integer" min="0" 
                                             max="3000" value="100" label="Minimum 
                                             length of poly-N to trim at the 5'-end" 
-                                            help=""/>
+                                            help="(-trim_ns_left)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                                 <conditional name="right_ns_tail_trimming_treatments">
                                     <param name='apply_right_ns_tail_trimming_treatments' 
-                                        type='boolean' checked="false" label="Trim 
+                                        type='boolean' checked="false" truevalue="true" 
+                                        falsevalue="false" label="Trim 
                                         poly-N tail at the 5'-end?" help="By default, 
                                         no 3'-end poly-N tail trimming is made"/>
                                     <when value="true">
@@ -541,46 +651,54 @@
                                             type="integer" min="0" 
                                             max="3000" value="100" label="Minimum 
                                             length of poly-N to trim at the 5'-end" 
-                                            help=""/>
+                                            help="(-trim_ns_right)"/>
                                     </when>
+                                    <when value="false" />
                                 </conditional>
                             </when>
+                            <when value="false" />
                         </conditional>
                     </when>
+                    <when value="false" />
                 </conditional>
                 <conditional name="quality_trimming_treatments">
                     <param name='apply_quality_trimming_treatments' type='boolean' 
-                        checked="true" label="Trim sequence by quality score?" 
+                        checked="true" truevalue="true" falsevalue="false" 
+                        label="Trim sequence by quality score?" 
                         help="By default, a 3'-end trimming is made to remove ends 
                         with a minimum quality score over 5 bp below 20"/>
                     <when value="true">
                         <conditional name="left_quality_trimming_treatments">
                             <param name='apply_left_quality_trimming_treatments' 
-                                type='boolean' checked="false" label="Trim sequence 
+                                type='boolean' checked="false" truevalue="true" 
+                                falsevalue="false" label="Trim sequence 
                                 by quality score from the 5'-end?" help="By default, 
                                 no 5'-end quality trimming is made"/>
                             <when value="true">
                                 <param name="left_quality_trimming_treatment_value" 
                                     type="integer" min="0" max="40" 
                                     value="20" label="Quality score threshold to 
-                                    trim positions" help=""/>
+                                    trim positions" help="(-trim_qual_left)"/>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <conditional name="right_quality_trimming_treatments">
                             <param name='apply_right_quality_trimming_treatments' 
-                                type='boolean' checked="true" label="Trim sequence 
+                                type='boolean' checked="true" truevalue="true" 
+                                falsevalue="false" label="Trim sequence 
                                 by quality score from the 3'-end?" help="By default,
                                  3'-end trimming is made based on a score of 20"/>
                             <when value="true">
                                 <param name="right_quality_trimming_treatment_value" 
                                     type="integer" min="0" max="40" 
                                     value="20" label="Quality score threshold to 
-                                    trim positions" help=""/>
+                                    trim positions" help="(-trim_qual_right)"/>
                             </when>
+                            <when value="false" />
                         </conditional>
                         <param name="type_quality_trimming_treatments" type="select" 
                             display="radio" label="Type of quality score calculation 
-                            to use" help="By default, min is used">
+                            to use" help="By default, min is used. (-trim_qual_type)">
                             <option value="min" selected="true">Mininum</option>
                             <option value="mean" >Mean</option>
                             <option value="max" >Max</option>
@@ -589,7 +707,7 @@
                         <param name="rule_quality_trimming_treatments" type="select" 
                             display="radio" label="Rule tu use to compare quality 
                             score to calculated value" help="By default, 'less than' 
-                            is used">
+                            is used. (-trim_qual_rule)">
                             <option value="lt" selected="true">Less than</option>
                             <option value="gt" >Greater than</option>
                             <option value="et" >Equal to</option>
@@ -598,26 +716,81 @@
                          min="0" max="300" value="1" label="Size of the sliding 
                          window used to calculated quality score by type" help="To 
                          stop at the first base that fails the rule defined, use a 
-                         window size of 1 (default value)"/>
+                         window size of 1 (default value). (-trim_qual_window)"/>
                         <param name="step_quality_trimming_treatments" type="integer" 
                             min="0" max="300" value="1" label="Step size used to move 
                             the sliding window" help="To move the window over all 
                             quality scores without missing any, the step size sould 
                             be less or equal to the window size. The default value 
-                            is 1."/>
+                            is 1. (-trim_qual_step)"/>
                     </when>
+                    <when value="false" />
                 </conditional>
             </when>
+            <when value="false" />
         </conditional>
+
+        <param name="graph_stats" type="select" multiple="True" label="Which statistics should be calculated included in the graph_data file" help="(-graph_stats)">
+            <option value="ld" selected="True">Length distribution</option>
+            <option value="gc" selected="True">GC content distribution</option>
+            <option value="qd" selected="True">Base quality distribution</option>
+            <option value="ns" selected="True">Occurence of N</option>
+            <option value="pt" selected="True">Poly-A/T tails</option>
+            <option value="ts" selected="True">Tag sequence check</option>
+            <option value="aq" selected="True">Assembly quality measure</option>
+            <option value="de" selected="True">Sequence duplication - exact only</option>
+            <option value="da" selected="True">Sequence duplication - exact + 5'/3'</option>
+            <option value="sc" selected="True">Sequence complexity</option>
+            <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
+        </param>
     </inputs>
 
     <outputs>
         <data format="fastq" name="good_sequence_file" 
             from_work_dir="good_sequences.fastq"
-            label="Good sequences of ${on_string} (PRINSEQ)" />
+            label="Good sequences of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "single"</filter>
+        </data>
         <data format="fastq" name="rejected_sequence_file" 
             from_work_dir="rejected_sequences.fastq"
-            label="Rejected sequences of ${on_string} (PRINSEQ)" />
+            label="Rejected sequences of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "single"</filter>
+        </data>
+
+        <data format="fastq" name="good_sequences_1_file" 
+            from_work_dir="good_sequences_1.fastq"
+            label="Good sequences for R1 of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "paired"</filter>
+        </data>
+        <data format="fastq" name="good_sequences_1_singletons_file" 
+            from_work_dir="good_sequences_1_singletons.fastq"
+            label="Good singleton sequences for R1 of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "paired"</filter>
+        </data>
+        <data format="fastq" name="rejected_sequence_1_file" 
+            from_work_dir="rejected_sequences_1.fastq"
+            label="Rejected sequences for R1 of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "paired"</filter>
+        </data>
+        <data format="fastq" name="good_sequences_2_file" 
+            from_work_dir="good_sequences_2.fastq"
+            label="Good sequences for R2 of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "paired"</filter>
+        </data>
+        <data format="fastq" name="good_sequences_2_singletons_file" 
+            from_work_dir="good_sequences_2_singletons.fastq"
+            label="Good singleton sequences for R2 of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "paired"</filter>
+        </data>
+        <data format="fastq" name="rejected_sequence_2_file" 
+            from_work_dir="rejected_sequences_2.fastq"
+            label="Rejected sequences for R2 of ${on_string} (PRINSEQ)" >
+            <filter>seq_type['seq_type_opt'] == "paired"</filter>
+        </data>
+
+        <data format="html" name="html_file" 
+            from_work_dir="stats_html.html"
+            label="Summary of ${tool.name} on ${on_string} summary" />
     </outputs>
 
     <tests>
@@ -682,16 +855,20 @@
 
 **Parameters**
 
-The parameters are numerous in PRINSEQ
+The parameters are numerous in PRINSEQ given the wanted treatments.
+
+Several filter treatments are proposed:
 
-    - Filtering parameters to eliminate sequences
-        - Filters based on sequence length 
-        - Filters based on quality score
-        - Filters based on base content
-    - Trimming parameters to eliminate sequence parts
-        - Trim of ends
-        - Trim of tails
-        - Trim based quality score
+ - Filters based on sequence length 
+ - Filters based on quality score
+ - Filters based on base content
+
+And several trimming treatments eliminate sequence parts:
+  - Trim of ends
+  - Trim of tails
+  - Trim based quality score
+
+All these treaments can be customed using the proposed parameters.
 
 -----
 
@@ -706,4 +883,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btr026</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r 10ac5c567b73 -r acaf871de2ea tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 17 06:02:09 2015 -0500
+++ b/tool_dependencies.xml	Wed Jan 27 03:55:09 2016 -0500
@@ -3,11 +3,15 @@
     <package name="prinseq" version="0.20.4">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/prinseq/standalone/prinseq-lite-0.20.4.tar.gz</action>
+                <action sha256sum="9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f" type="download_by_url">http://downloads.sourceforge.net/project/prinseq/standalone/prinseq-lite-0.20.4.tar.gz</action>
                 <action type="move_file">
                     <source>prinseq-lite.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
+                <action type="move_file">
+                    <source>prinseq-graphs-noPCA.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
                 <action type="set_environment">
                     <environment_variable name="PRINSEQ_DIR" action="set_to">$INSTALL_DIR/</environment_variable>
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>