Mercurial > repos > iuc > prinseq
view prinseq.xml @ 2:74afc47f326c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
| author | iuc |
|---|---|
| date | Fri, 03 Mar 2017 14:58:49 -0500 |
| parents | 6b865dde1baa |
| children | 02befcb391f5 |
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<tool id="prinseq" name="PRINSEQ" version="0.20.4"> <description>to process quality of sequences</description> <requirements> <requirement type="package" version="0.20.4">prinseq</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="" /> <regex match="ERROR" source="stderr" level="fatal" description="" /> <regex match="WARNING" source="stderr" level="warning" description="" /> </stdio> <version_command> <![CDATA[ prinseq-lite.pl --version ]]> </version_command> <command> <![CDATA[ mkdir tmp/ && prinseq-lite.pl #if $seq_type.seq_type_opt == "single": -fastq '$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' #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.is_of_type('fastqillumina'): -phred64 #end if #end if -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences" #if $filter_treatments.apply_filter_treatments == "true": #set length_filter_treatments=$filter_treatments.length_filter_treatments #if $length_filter_treatments.apply_length_filter_treatments == "true": #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments #if $min_length_filter_treatments.apply_min_length_filter_treatments == "true": -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 == "true": -max_len $max_length_filter_treatments.max_length_filter_treatment_value #end if #end if #set quality_filter_treatments=$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 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true": -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value #end if #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments #if $max_quality_filter_treatments.apply_max_quality_filter_treatments == "true": -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 $mean_quality_filter_treatments.apply_mean_quality_filter_treatments == "true": #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments == "true": -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 == "true": -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value #end if #end if #end if #set base_content_filter_treatments=$filter_treatments.base_content_filter_treatments #if $base_content_filter_treatments.apply_base_content_filter_treatments == "true": #set GC_perc_content_filter_treatments=$base_content_filter_treatments.GC_perc_content_filter_treatments #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments == "true": #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments == "true": -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 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments == "true": -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 == "true": -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 == "true": -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value #end if $base_content_filter_treatments.apply_other_base_content_filter_treatments #end if #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments #if $complexity_filter_treatments.apply_complexity_filter_treatments == "true": -lc_method $complexity_filter_treatments.method_complexity_filter_treatments -lc_threshold $complexity_filter_treatments.threshold_complexity_filter_treatments #end if #end if #if $trimming_treatments.apply_trimming_treatments == "true": #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments #if $length_trimming_treatments.apply_length_trimming_treatments == "true": -trim_to_len $length_trimming_treatments.length_trimming_treatment_value #end if #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments #if $position_trimming_treatments.apply_position_trimming_treatments == "true": #set nb_position_trimming_treatments=$position_trimming_treatments.nb_position_trimming_treatments #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments == "true": #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments #if $left_position_trimming_treatments.apply_left_position_trimming_treatments == "true": -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 == "true": -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 $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments == "true": #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments == "true": -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 == "true": -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value #end if #end if #end if #set tail_trimming_treatments=$trimming_treatments.tail_trimming_treatments #if $tail_trimming_treatments.apply_tail_trimming_treatments == "true": #set a_t_tail_trimming_treatments=$tail_trimming_treatments.a_t_tail_trimming_treatments #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments == "true": #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments == "true": -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 == "true": -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 $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments == "true": #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments == "true": -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 == "true": -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value #end if #end if #end if #set quality_trimming_treatments=$trimming_treatments.quality_trimming_treatments #if $quality_trimming_treatments.apply_quality_trimming_treatments == "true": #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments == "true": -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 == "true": -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 $quality_trimming_treatments.step_quality_trimming_treatments #end if #end if #* -graph_stats "$graph_stats" -graph_data tmp/stats.gd && prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html *# ]]> </command> <inputs> <conditional name="seq_type"> <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?"> <option value="single" selected="true">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="select" label="Apply filter treatments?"> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <conditional name="length_filter_treatments"> <param name="apply_length_filter_treatments" type="select" label="Filter sequence based on their length?" help="By default, sequences smaller than 60 bp are removed. No top threshold is defined"> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <conditional name="min_length_filter_treatments"> <param name="apply_min_length_filter_treatments" type="select" label="Filter too small sequences?" help="By default, sequences smaller than 60 bp are removed."> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <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 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> <option value="false" selected="true">No</option> </param> <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="(-max_len)"/> </when> <when value="false" /> </conditional> </when> <when value="false" /> </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> <option value="false">No</option> </param> <when value="true"> <conditional name="min_quality_filter_treatments"> <param name="apply_min_quality_filter_treatments" type="select" label="Filter sequences based on their minimum score?" help="By default, no treatment based on a minimum score is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <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="(-min_qual_score)"/> </when> <when value="false" /> </conditional> <conditional name="max_quality_filter_treatments"> <param name="apply_max_quality_filter_treatments" type="select" label="Filter sequences based on their maximum score?" help="By default, no treatment based on a minimum score is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <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="(-max_qual_score)"/> </when> <when value="false" /> </conditional> <conditional name="mean_quality_filter_treatments"> <param name="apply_mean_quality_filter_treatments" type="select" label="Filter sequences based on their mean score?" help="By default, sequences with a mean score below 15 are removed."> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <conditional name="min_mean_quality_filter_treatments"> <param name="apply_min_mean_quality_filter_treatments" type="select" label="Filter sequences based with too small mean score?" help="By default, sequences with a mean score below 15 are removed."> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <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" /> </conditional> <conditional name="max_mean_quality_filter_treatments"> <param name="apply_max_mean_quality_filter_treatments" type="select" label="Filter sequences based with too high mean score?" help="By default, no treatment based on a maximum mean score is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <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" /> </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="select" label="Filter sequences based on their base content?" help="By default, sequences with more than 2% of N bases are removed."> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <conditional name="GC_perc_content_filter_treatments"> <param name="apply_GC_perc_content_filter_treatments" type="select" label="Filter sequences based on their GC percentage?" help="By default, no treatment based on GC percentage is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="min_GC_perc_content_filter_treatments"> <param name="apply_min_GC_perc_content_filter_treatments" type="select" label="Filter sequences with too small GC percentage?" help="By default, no treatment based on GC percentage is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="min_GC_perc_content_filter_treatment_value" type="integer" min="0" max="100" value="10" label="Minimal GC percentage threshold to conserve 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="select" label="Filter sequences with too high GC percentage?" help="By default, no treatment based on GC percentage is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="max_GC_perc_content_filter_treatment_value" type="integer" min="0" max="100" value="90" label="Maximal GC percentage threshold to conserve 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="select" label="Filter sequences based on their number of N bases?" help="By default, no treatment based on N number is made."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <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="(-ns_max_n)"/> </when> <when value="false" /> </conditional> <conditional name="N_percentage_content_filter_treatments"> <param name="apply_N_percentage_content_filter_treatments" type="select" label="Filter sequences based on their percentage of N bases?" help="By default, sequences with more than 2% of N bases are removed."> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <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="(-ns_max_p)"/> </when> <when value="false" /> </conditional> <param name='apply_other_base_content_filter_treatments' 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. (-noniupac)"/> </when> <when value="false" /> </conditional> <conditional name="complexity_filter_treatments"> <param name="apply_complexity_filter_treatments" type="select" label="Filter sequences based on their complexity?" help="By default, no complexity filter is applied."> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <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 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 name="trimming_treatments"> <param name="apply_trimming_treatments" type="select" label="Apply trimming treatments?" help=""> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <conditional name="length_trimming_treatments"> <param name="apply_length_trimming_treatments" type="select" label="Trim all sequences from the 3'-end to a defined length?" help="By default, no length trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Length of sequences after trimming" help="(-trim_to_len)"/> </when> <when value="false" /> </conditional> <conditional name="position_trimming_treatments"> <param name="apply_position_trimming_treatments" type="select" label="Trim all sequences from the ends?" help="By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="nb_position_trimming_treatments"> <param name="apply_nb_position_trimming_treatments" type="select" label="Trim sequences by a defined number of positions?" help="By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="left_position_trimming_treatments"> <param name="apply_left_position_trimming_treatments" type="select" label="Trim sequences at the 5'-end by a defined number of positions?" help="By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <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="(-trim_left)"/> </when> <when value="false" /> </conditional> <conditional name="right_position_trimming_treatments"> <param name="apply_right_position_trimming_treatments" type="select" label="Trim sequences at the 3'-end by a defined number of positions?" help="By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="right_position_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 3'-end" 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="select" label="Trim sequences by a defined percentage of read length?" help="The trim length is rounded towards the lower integer. By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="left_percentage_position_trimming_treatments"> <param name="apply_left_percentage_position_trimming_treatments" type="select" label="Trim sequences at the 5'-end by a defined percentage of read length?" help="The trim length is rounded towards the lower integer. By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <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="(-trim_left_p)"/> </when> <when value="false" /> </conditional> <conditional name="right_percentage_position_trimming_treatments"> <param name="apply_right_percentage_position_trimming_treatments" type="select" label="Trim sequences at the 3'-end by a defined percentage of read length?" help="The trim length is rounded towards the lower integer. By default, no position trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <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="(-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="select" label="Trim tails?" help="By default, no tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="a_t_tail_trimming_treatments"> <param name="apply_a_t_tail_trimming_treatments" type="select" label="Trim poly-A/T tail?" help="By default, no poly-A/T tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="left_a_t_tail_trimming_treatments"> <param name="apply_left_a_t_tail_trimming_treatments" type="select" label="Trim poly-A/T tail at the 5'-end?" help="By default, no 5'-end poly-A/T tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="left_a_t_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" 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="select" label="Trim poly-A/T tail at the 3'-end?" help="By default, no 3'-end poly-A/T tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="right_a_t_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" 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="select" label="Trim poly-N tail?" help="By default, no poly-N tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <conditional name="left_ns_tail_trimming_treatments"> <param name="apply_left_ns_tail_trimming_treatments" type="select" label="Trim poly-N tail at the 5'-end?" help="By default, no 5'-end poly-N tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="left_ns_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" 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="select" label="Trim poly-N tail at the 3'-end?" help="By default, no 3'-end poly-N tail trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> <param name="right_ns_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" 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="select" 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"> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <when value="true"> <conditional name="left_quality_trimming_treatments"> <param name="apply_left_quality_trimming_treatments" type="select" label="Trim sequence by quality score from the 5'-end?" help="By default, no 5'-end quality trimming is made"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <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_qual_left)"/> </when> <when value="false" /> </conditional> <conditional name="right_quality_trimming_treatments"> <param name="apply_right_quality_trimming_treatments" type="select" label="Trim sequence by quality score from the 3'-end?" help="By default, 3'-end trimming is made based on a score of 20"> <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> <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_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. (-trim_qual_type)"> <option value="min" selected="true">Mininum</option> <option value="mean" >Mean</option> <option value="max" >Max</option> <option value="sum" >Sum</option> </param> <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. (-trim_qual_rule)"> <option value="lt" selected="true">Less than</option> <option value="gt" >Greater than</option> <option value="et" >Equal to</option> </param> <param name="window_quality_trimming_treatments" type="integer" 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). (-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. (-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="tmp/good_sequences.fastq" label="${tool.name} on ${on_string}: Good sequences" > <filter>seq_type['seq_type_opt'] == "single"</filter> </data> <data format="fastq" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq" label="${tool.name} on ${on_string}: Rejected sequences" > <filter>seq_type['seq_type_opt'] == "single"</filter> </data> <data format="fastq" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq" label="${tool.name} on ${on_string}: Good sequences for R1" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> <data format="fastq" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq" label="${tool.name} on ${on_string}: Good singleton sequences for R1" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> <data format="fastq" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq" label="${tool.name} on ${on_string}: Rejected sequences for R1" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> <data format="fastq" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq" label="${tool.name} on ${on_string}: Good sequences for R2" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> <data format="fastq" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq" label="${tool.name} on ${on_string}: Good singleton sequences for R2" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> <data format="fastq" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq" label="${tool.name} on ${on_string}: Rejected sequences for R2" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> <!--<data format="html" name="html_file" from_work_dir="stats_html.html" label="${tool.name} on ${on_string}: Summary" />--> </outputs> <tests> <test> <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="min_length_filter_treatment_value" value="60"/> <param name='apply_max_length_filter_treatments' value="false" /> <param name='apply_quality_filter_treatments' value="true"/> <param name='apply_min_quality_filter_treatments' value="false" /> <param name='apply_max_quality_filter_treatments' value="false"/> <param name='apply_mean_quality_filter_treatments' value="true"/> <param name='apply_min_mean_quality_filter_treatments' value="true"/> <param name="min_mean_quality_filter_treatment_value" value="15"/> <param name='apply_max_mean_quality_filter_treatments' value="false"/> <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="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"/> <param name='apply_trimming_treatments' value="true" /> <param name='apply_length_trimming_treatments' value="false"/> <param name='apply_position_trimming_treatments' value="false"/> <param name='apply_tail_trimming_treatments' value="false"/> <param name='apply_quality_trimming_treatments' value="true"/> <param name='apply_left_quality_trimming_treatments' value="false"/> <param name='apply_right_quality_trimming_treatments' value="true" /> <param name="right_quality_trimming_treatment_value" value="20"/> <param name="type_quality_trimming_treatments" value="min"/> <param name="rule_quality_trimming_treatments" value="lt" /> <param name="window_quality_trimming_treatments" value="1"/> <param name="step_quality_trimming_treatments" value="1"/> <output name="good_sequence_file" file="prinseq_good_sequences.fastq"/> </test> </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. More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_. ----- **Input** The input file is sequence file in fastq format (sequences and quality):: @HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT + CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF ----- **Parameters** The parameters are numerous in PRINSEQ given the wanted treatments. Several filter treatments are proposed: - 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 proposed parameters. ----- **Output** The output file is a sequence file with sequences and quality from input file which have undergone filter and trimming. ]]> </help> <citations> <citation type="doi">10.1093/bioinformatics/btr026</citation> </citations> </tool>