prinseq: prinseq.xml annotate

author	iuc
date	Tue, 31 May 2016 07:43:42 -0400
parents
children	6b865dde1baa

rev	line source
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	1 <tool id="prinseq" name="PRINSEQ" version="0.1.0">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	2 <description>to process quality of sequences</description>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	3
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	4 <requirements>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	5 <requirement type="package" version="5.18.1">perl</requirement>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	6 <!--<requirement type="package" version="2.90">perl-json</requirement>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	7 <requirement type="package" version="1.106">perl-cairo</requirement>-->
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	8 <requirement type="package" version="0.20.4">prinseq</requirement>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	9 </requirements>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	10
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	11 <stdio>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	12 <exit_code range="1:" level="fatal" description="" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	13 <regex match="ERROR"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	14 source="stderr"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	15 level="fatal"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	16 description="" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	17 <regex match="WARNING"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	18 source="stderr"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	19 level="warning"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	20 description="" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	21 </stdio>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	22
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	23 <version_command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	24 <![CDATA[
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	25 prinseq-lite.pl --version
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	26 ]]>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	27 </version_command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	28
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	29 <command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	30 <![CDATA[
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	31 mkdir tmp/
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	32
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	33 &&
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	34
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	35 prinseq-lite.pl
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	36 #if $seq_type.seq_type_opt == "single":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	37 -fastq "$seq_type.input_singles"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	38 #if $seq_type.input_singles.ext == "fastqillumina":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	39 -phred64
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	40 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	41 #else:
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	42 -fastq "$seq_type.input_mate1"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	43 -fastq2 "$seq_type.input_mate2"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	44 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	45 #import sys
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	46 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	47 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	48 #if $seq_type.input_mate1.ext == "fastqillumina":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	49 -phred64
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	50 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	51 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	52
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	53 -out_good "tmp/good_sequences"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	54 -out_bad "tmp/rejected_sequences"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	55
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	56 #if $filter_treatments.apply_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	57 #set length_filter_treatments=$filter_treatments.length_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	58 #if $length_filter_treatments.apply_length_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	59 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	60 #if $min_length_filter_treatments.apply_min_length_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	61 -min_len $min_length_filter_treatments.min_length_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	62 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	63
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	64 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	65 #if $max_length_filter_treatments.apply_max_length_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	66 -max_len $max_length_filter_treatments.max_length_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	67 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	68 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	69
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	70 #set quality_filter_treatments=$filter_treatments.quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	71 #if $quality_filter_treatments.apply_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	72 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	73 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	74 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	75 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	76
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	77 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	78 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	79 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	80 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	81
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	82 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	83 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	84 #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	85 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	86 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	87 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	88
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	89 #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	90 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	91 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	92 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	93 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	94 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	95
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	96 #set base_content_filter_treatments=$filter_treatments.base_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	97 #if $base_content_filter_treatments.apply_base_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	98 #set GC_perc_content_filter_treatments=$base_content_filter_treatments.GC_perc_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	99 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	100 #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	101 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	102 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	103 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	104
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	105 #set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	106 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	107 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	108 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	109 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	110
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	111 #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	112 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	113 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	114 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	115
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	116 #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	117 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	118 -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	119 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	120
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	121 $base_content_filter_treatments.apply_other_base_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	122 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	123
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	124 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	125 #if $complexity_filter_treatments.apply_complexity_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	126 -lc_method $complexity_filter_treatments.method_complexity_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	127 -lc_threshold $complexity_filter_treatments.threshold_complexity_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	128 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	129
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	130 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	131
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	132 #if $trimming_treatments.apply_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	133 #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	134 #if $length_trimming_treatments.apply_length_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	135 -trim_to_len $length_trimming_treatments.length_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	136 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	137
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	138 #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	139 #if $position_trimming_treatments.apply_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	140 #set nb_position_trimming_treatments=$position_trimming_treatments.nb_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	141 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	142 #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	143 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	144 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	145 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	146
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	147 #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	148 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	149 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	150 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	151 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	152
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	153 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	154 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	155 #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	156 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	157 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	158 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	159
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	160 #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	161 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	162 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	163 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	164 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	165 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	166
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	167 #set tail_trimming_treatments=$trimming_treatments.tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	168 #if $tail_trimming_treatments.apply_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	169 #set a_t_tail_trimming_treatments=$tail_trimming_treatments.a_t_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	170 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	171 #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	172 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	173 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	174 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	175
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	176 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	177 #if $right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	178 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	179 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	180 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	181
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	182 #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	183 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	184 #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	185 #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	186 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	187 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	188
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	189 #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	190 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	191 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	192 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	193 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	194 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	195
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	196 #set quality_trimming_treatments=$trimming_treatments.quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	197 #if $quality_trimming_treatments.apply_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	198 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	199 #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	200 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	201 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	202
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	203 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	204 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	205 -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	206 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	207
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	208 -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	209 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	210 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	211 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	212 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	213
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	214 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	215
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	216 #*
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	217 -graph_stats "$graph_stats"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	218 -graph_data tmp/stats.gd
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	219
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	220
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	221 &&
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	222
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	223 prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	224 *#
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	225 ]]>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	226 </command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	227
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	228 <inputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	229 <conditional name="seq_type">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	230 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	231 <option value="single" selected="true">Single-end</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	232 <option value="paired">Paired-end</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	233 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	234 <when value="single">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	235 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	236 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	237 <when value="paired">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	238 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	239 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	240 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	241 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	242
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	243 <conditional name="filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	244 <param name="apply_filter_treatments" type="select" label="Apply filter treatments?">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	245 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	246 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	247 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	248 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	249 <conditional name="length_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	250 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	251 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	252 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	253 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	254 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	255 <conditional name="min_length_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	256 <param name="apply_min_length_filter_treatments" type="select" label="Filter too small sequences?" help="By default, sequences smaller than 60 bp are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	257 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	258 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	259 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	260 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	261 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	262 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	263 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	264 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	265 <conditional name="max_length_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	266 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	267 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	268 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	269 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	270 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	271 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	272 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	273 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	274 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	275 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	276 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	277 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	278 <conditional name="quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	279 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	280 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	281 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	282 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	283 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	284 <conditional name="min_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	285 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	286 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	287 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	288 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	289 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	290 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	291 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	292 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	293 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	294 <conditional name="max_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	295 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	296 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	297 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	298 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	299 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	300 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	301 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	302 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	303 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	304 <conditional name="mean_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	305 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	306 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	307 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	308 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	309 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	310 <conditional name="min_mean_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	311 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	312 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	313 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	314 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	315 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	316 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	317 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	318 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	319 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	320 <conditional name="max_mean_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	321 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	322 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	323 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	324 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	325 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	326 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	327 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	328 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	329 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	330 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	331 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	332 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	333 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	334 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	335 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	336 <conditional name="base_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	337 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	338 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	339 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	340 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	341 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	342 <conditional name="GC_perc_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	343 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	344 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	345 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	346 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	347 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	348 <conditional name="min_GC_perc_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	349 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	350 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	351 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	352 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	353 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	354 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	355 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	356 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	357 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	358 <conditional name="max_GC_perc_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	359 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	360 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	361 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	362 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	363 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	364 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	365 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	366 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	367 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	368 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	369 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	370 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	371 <conditional name="N_number_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	372 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	373 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	374 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	375 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	376 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	377 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	378 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	379 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	380 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	381 <conditional name="N_percentage_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	382 <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.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	383 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	384 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	385 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	386 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	387 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	388 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	389 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	390 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	391 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	392 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	393 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	394 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	395 <conditional name="complexity_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	396 <param name="apply_complexity_filter_treatments" type="select" label="Filter sequences based on their complexity?" help="By default, no complexity filter is applied.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	397 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	398 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	399 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	400 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	401 <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help="(-lc_method)">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	402 <option value="dust">Dust</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	403 <option value="entropy" >Entropy</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	404 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	405 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	406 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	407 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	408 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	409 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	410 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	411 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	412
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	413 <conditional name="trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	414 <param name="apply_trimming_treatments" type="select" label="Apply trimming treatments?" help="">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	415 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	416 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	417 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	418 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	419 <conditional name="length_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	420 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	421 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	422 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	423 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	424 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	425 <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Length of sequences after trimming" help="(-trim_to_len)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	426 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	427 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	428 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	429 <conditional name="position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	430 <param name="apply_position_trimming_treatments" type="select" label="Trim all sequences from the ends?" help="By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	431 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	432 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	433 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	434 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	435 <conditional name="nb_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	436 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	437 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	438 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	439 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	440 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	441 <conditional name="left_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	442 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	443 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	444 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	445 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	446 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	447 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	448 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	449 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	450 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	451 <conditional name="right_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	452 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	453 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	454 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	455 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	456 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	457 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	458 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	459 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	460 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	461 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	462 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	463 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	464 <conditional name="percentage_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	465 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	466 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	467 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	468 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	469 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	470 <conditional name="left_percentage_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	471 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	472 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	473 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	474 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	475 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	476 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	477 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	478 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	479 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	480 <conditional name="right_percentage_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	481 <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">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	482 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	483 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	484 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	485 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	486 <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)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	487 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	488 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	489 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	490 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	491 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	492 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	493 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	494 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	495 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	496 <conditional name="tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	497 <param name="apply_tail_trimming_treatments" type="select" label="Trim tails?" help="By default, no tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	498 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	499 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	500 </param>

0

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

1 <tool id="prinseq" name="PRINSEQ" version="0.1.0">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

2 <description>to process quality of sequences</description>

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diff changeset

3

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

4 <requirements>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

5 <requirement type="package" version="5.18.1">perl</requirement>

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6 <!--<requirement type="package" version="2.90">perl-json</requirement>

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7 <requirement type="package" version="1.106">perl-cairo</requirement>-->

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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8 <requirement type="package" version="0.20.4">prinseq</requirement>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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9 </requirements>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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10

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11 <stdio>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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12 <exit_code range="1:" level="fatal" description="" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

13 <regex match="ERROR"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

14 source="stderr"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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15 level="fatal"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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16 description="" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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17 <regex match="WARNING"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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18 source="stderr"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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19 level="warning"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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20 description="" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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21 </stdio>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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22

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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23 <version_command>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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24 <![CDATA[

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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25 prinseq-lite.pl --version

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26 ]]>

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27 </version_command>

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28

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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29 <command>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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30 <![CDATA[

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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31 mkdir tmp/

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32

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33 &&

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34

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35 prinseq-lite.pl

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36 #if $seq_type.seq_type_opt == "single":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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37 -fastq "$seq_type.input_singles"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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38 #if $seq_type.input_singles.ext == "fastqillumina":

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39 -phred64

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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40 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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41 #else:

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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42 -fastq "$seq_type.input_mate1"

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43 -fastq2 "$seq_type.input_mate2"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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44 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:

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45 #import sys

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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46 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )

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47 #end if

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48 #if $seq_type.input_mate1.ext == "fastqillumina":

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49 -phred64

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50 #end if

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51 #end if

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52

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diff changeset

53 -out_good "tmp/good_sequences"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

54 -out_bad "tmp/rejected_sequences"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

55

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

56 #if $filter_treatments.apply_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

57 #set length_filter_treatments=$filter_treatments.length_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

58 #if $length_filter_treatments.apply_length_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

59 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

60 #if $min_length_filter_treatments.apply_min_length_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

61 -min_len $min_length_filter_treatments.min_length_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

62 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

63

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

64 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

65 #if $max_length_filter_treatments.apply_max_length_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

66 -max_len $max_length_filter_treatments.max_length_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

67 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

68 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

69

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

70 #set quality_filter_treatments=$filter_treatments.quality_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

71 #if $quality_filter_treatments.apply_quality_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

72 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

73 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

74 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

75 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

76

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

77 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

78 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

79 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

80 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

81

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

82 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

83 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

84 #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

85 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

86 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

87 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

88

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

89 #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

90 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

91 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

92 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

93 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

94 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

95

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

96 #set base_content_filter_treatments=$filter_treatments.base_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

97 #if $base_content_filter_treatments.apply_base_content_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

98 #set GC_perc_content_filter_treatments=$base_content_filter_treatments.GC_perc_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

99 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

100 #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

101 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

102 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

103 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

104

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

105 #set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

106 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

107 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

108 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

109 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

110

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

111 #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

112 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

113 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

114 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

115

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

116 #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

117 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

118 -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

119 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

120

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

121 $base_content_filter_treatments.apply_other_base_content_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

122 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

123

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

124 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

125 #if $complexity_filter_treatments.apply_complexity_filter_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

126 -lc_method $complexity_filter_treatments.method_complexity_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

127 -lc_threshold $complexity_filter_treatments.threshold_complexity_filter_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

128 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

129

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

130 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

131

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

132 #if $trimming_treatments.apply_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

133 #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

134 #if $length_trimming_treatments.apply_length_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

135 -trim_to_len $length_trimming_treatments.length_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

136 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

137

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

138 #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

139 #if $position_trimming_treatments.apply_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

140 #set nb_position_trimming_treatments=$position_trimming_treatments.nb_position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

141 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

142 #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

143 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

144 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

145 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

146

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

147 #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

148 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

149 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

150 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

151 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

152

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

153 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

154 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

155 #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

156 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

157 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

158 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

159

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

160 #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

161 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

162 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

163 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

164 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

165 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

166

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

167 #set tail_trimming_treatments=$trimming_treatments.tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

168 #if $tail_trimming_treatments.apply_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

169 #set a_t_tail_trimming_treatments=$tail_trimming_treatments.a_t_tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

170 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

171 #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

172 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

173 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

174 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

175

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

176 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

177 #if $right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

178 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

179 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

180 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

181

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

182 #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

183 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

184 #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

185 #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

186 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

187 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

188

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

189 #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

190 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

191 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

192 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

193 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

194 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

195

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

196 #set quality_trimming_treatments=$trimming_treatments.quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

197 #if $quality_trimming_treatments.apply_quality_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

198 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

199 #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

200 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

201 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

202

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

203 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

204 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments == "true":

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

205 -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

206 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

207

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

208 -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

209 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

210 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

211 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

212 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

213

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

214 #end if

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

215

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

216 #*

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

217 -graph_stats "$graph_stats"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

218 -graph_data tmp/stats.gd

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

219

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

220

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

221 &&

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

222

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223 prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html

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224 *#

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225 ]]>

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226 </command>

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227

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228 <inputs>

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229 <conditional name="seq_type">

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230 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">

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231 <option value="single" selected="true">Single-end</option>

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232 <option value="paired">Paired-end</option>

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233 </param>

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234 <when value="single">

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235 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />

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236 </when>

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237 <when value="paired">

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238 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />

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239 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />

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240 </when>

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241 </conditional>

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242

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243 <conditional name="filter_treatments">

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244 <param name="apply_filter_treatments" type="select" label="Apply filter treatments?">

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245 <option value="true" selected="true">Yes</option>

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246 <option value="false">No</option>

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247 </param>

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248 <when value="true">

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249 <conditional name="length_filter_treatments">

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250 <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">

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251 <option value="true" selected="true">Yes</option>

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252 <option value="false">No</option>

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253 </param>

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254 <when value="true">

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255 <conditional name="min_length_filter_treatments">

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256 <param name="apply_min_length_filter_treatments" type="select" label="Filter too small sequences?" help="By default, sequences smaller than 60 bp are removed.">

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257 <option value="true" selected="true">Yes</option>

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258 <option value="false">No</option>

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259 </param>

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260 <when value="true">

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261 <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)"/>

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262 </when>

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263 <when value="false" />

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264 </conditional>

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265 <conditional name="max_length_filter_treatments">

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266 <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.">

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267 <option value="true">Yes</option>

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268 <option value="false" selected="true">No</option>

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269 </param>

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270 <when value="true">

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271 <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)"/>

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272 </when>

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273 <when value="false" />

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274 </conditional>

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275 </when>

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276 <when value="false" />

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277 </conditional>

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278 <conditional name="quality_filter_treatments">

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279 <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.">

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280 <option value="true" selected="true">Yes</option>

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281 <option value="false">No</option>

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282 </param>

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283 <when value="true">

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284 <conditional name="min_quality_filter_treatments">

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285 <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.">

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286 <option value="true">Yes</option>

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287 <option value="false" selected="true">No</option>

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288 </param>

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289 <when value="true">

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290 <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)"/>

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291 </when>

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292 <when value="false" />

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293 </conditional>

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294 <conditional name="max_quality_filter_treatments">

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295 <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.">

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296 <option value="true">Yes</option>

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297 <option value="false" selected="true">No</option>

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298 </param>

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299 <when value="true">

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300 <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)"/>

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301 </when>

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diff changeset

302 <when value="false" />

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303 </conditional>

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304 <conditional name="mean_quality_filter_treatments">

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305 <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.">

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306 <option value="true" selected="true">Yes</option>

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307 <option value="false">No</option>

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308 </param>

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309 <when value="true">

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diff changeset

310 <conditional name="min_mean_quality_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

311 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

312 <option value="true" selected="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

313 <option value="false">No</option>

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parents:

diff changeset

314 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

315 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

316 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

317 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

318 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

319 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

320 <conditional name="max_mean_quality_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

321 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

322 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

323 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

324 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

325 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

326 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

327 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

328 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

329 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

330 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

331 <when value="false" />

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parents:

diff changeset

332 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

333 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

334 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

335 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

336 <conditional name="base_content_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

337 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

338 <option value="true" selected="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

339 <option value="false">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

340 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

341 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

342 <conditional name="GC_perc_content_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

343 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

344 <option value="true">Yes</option>

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iuc

parents:

diff changeset

345 <option value="false" selected="true">No</option>

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parents:

diff changeset

346 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

347 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

348 <conditional name="min_GC_perc_content_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

349 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

350 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

351 <option value="false" selected="true">No</option>

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parents:

diff changeset

352 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

353 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

354 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

355 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

356 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

357 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

358 <conditional name="max_GC_perc_content_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

359 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

360 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

361 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

362 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

363 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

364 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

365 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

366 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

367 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

368 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

369 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

370 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

371 <conditional name="N_number_content_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

372 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

373 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

374 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

375 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

376 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

377 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

378 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

379 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

380 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

381 <conditional name="N_percentage_content_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

382 <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.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

383 <option value="true" selected="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

384 <option value="false">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

385 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

386 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

387 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

388 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

389 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

390 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

391 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

392 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

393 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

394 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

395 <conditional name="complexity_filter_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

396 <param name="apply_complexity_filter_treatments" type="select" label="Filter sequences based on their complexity?" help="By default, no complexity filter is applied.">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

397 <option value="true">Yes</option>

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parents:

diff changeset

398 <option value="false" selected="true">No</option>

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parents:

diff changeset

399 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

400 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

401 <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help="(-lc_method)">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

402 <option value="dust">Dust</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

403 <option value="entropy" >Entropy</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

404 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

405 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

406 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

407 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

408 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

409 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

410 <when value="false" />

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parents:

diff changeset

411 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

412

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

413 <conditional name="trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

414 <param name="apply_trimming_treatments" type="select" label="Apply trimming treatments?" help="">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

415 <option value="true" selected="true">Yes</option>

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iuc

parents:

diff changeset

416 <option value="false">No</option>

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iuc

parents:

diff changeset

417 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

418 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

419 <conditional name="length_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

420 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

421 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

422 <option value="false" selected="true">No</option>

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iuc

parents:

diff changeset

423 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

424 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

425 <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Length of sequences after trimming" help="(-trim_to_len)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

426 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

427 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

428 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

429 <conditional name="position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

430 <param name="apply_position_trimming_treatments" type="select" label="Trim all sequences from the ends?" help="By default, no position trimming is made">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

431 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

432 <option value="false" selected="true">No</option>

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parents:

diff changeset

433 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

434 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

435 <conditional name="nb_position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

436 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

437 <option value="true">Yes</option>

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iuc

parents:

diff changeset

438 <option value="false" selected="true">No</option>

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parents:

diff changeset

439 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

440 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

441 <conditional name="left_position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

442 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

443 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

444 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

445 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

446 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

447 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

448 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

449 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

450 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

451 <conditional name="right_position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

452 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

453 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

454 <option value="false" selected="true">No</option>

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parents:

diff changeset

455 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

456 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

457 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

458 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

459 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

460 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

461 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

462 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

463 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

464 <conditional name="percentage_position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

465 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

466 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

467 <option value="false" selected="true">No</option>

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parents:

diff changeset

468 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

469 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

470 <conditional name="left_percentage_position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

471 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

472 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

473 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

474 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

475 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

476 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

477 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

478 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

479 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

480 <conditional name="right_percentage_position_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

481 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

482 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

483 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

484 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

485 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

486 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

487 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

488 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

489 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

490 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

491 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

492 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

493 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

494 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

495 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

496 <conditional name="tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

497 <param name="apply_tail_trimming_treatments" type="select" label="Trim tails?" help="By default, no tail trimming is made">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

498 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

499 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

500 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

501 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

502 <conditional name="a_t_tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

503 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

504 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

505 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

506 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

507 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

508 <conditional name="left_a_t_tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

509 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

510 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

511 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

512 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

513 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

514 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

515 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

516 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

517 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

518 <conditional name="right_a_t_tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

519 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

520 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

521 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

522 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

523 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

524 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

525 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

526 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

527 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

528 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

529 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

530 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

531 <conditional name="ns_tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

532 <param name="apply_ns_tail_trimming_treatments" type="select" label="Trim poly-N tail?" help="By default, no poly-N tail trimming is made">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

533 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

534 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

535 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

536 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

537 <conditional name="left_ns_tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

538 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

539 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

540 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

541 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

542 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

543 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

544 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

545 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

546 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

547 <conditional name="right_ns_tail_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

548 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

549 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

550 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

551 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

552 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

553 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

554 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

555 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

556 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

557 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

558 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

559 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

560 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

561 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

562 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

563 <conditional name="quality_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

564 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

565 <option value="true" selected="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

566 <option value="false">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

567 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

568 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

569 <conditional name="left_quality_trimming_treatments">

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iuc

parents:

diff changeset

570 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

571 <option value="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

572 <option value="false" selected="true">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

573 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

574 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

575 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

576 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

577 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

578 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

579 <conditional name="right_quality_trimming_treatments">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

580 <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">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

581 <option value="true" selected="true">Yes</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

582 <option value="false">No</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

583 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

584 <when value="true">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

585 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

586 </when>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

587 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

588 </conditional>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

589 <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)">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

590 <option value="min" selected="true">Mininum</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

591 <option value="mean" >Mean</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

592 <option value="max" >Max</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

593 <option value="sum" >Sum</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

594 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

595 <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)">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

596 <option value="lt" selected="true">Less than</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

597 <option value="gt" >Greater than</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

598 <option value="et" >Equal to</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

599 </param>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

600 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

601 <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)"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

602 </when>

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parents:

diff changeset

603 <when value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

604 </conditional>

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diff changeset

605 </when>

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diff changeset

606 <when value="false" />

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diff changeset

607 </conditional>

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diff changeset

608

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diff changeset

609 <!--<param name="graph_stats" type="select" multiple="True" label="Which statistics should be calculated included in the graph_data file" help="(-graph_stats)">

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

610 <option value="ld" selected="True">Length distribution</option>

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parents:

diff changeset

611 <option value="gc" selected="True">GC content distribution</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

612 <option value="qd" selected="True">Base quality distribution</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

613 <option value="ns" selected="True">Occurence of N</option>

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parents:

diff changeset

614 <option value="pt" selected="True">Poly-A/T tails</option>

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parents:

diff changeset

615 <option value="ts" selected="True">Tag sequence check</option>

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parents:

diff changeset

616 <option value="aq" selected="True">Assembly quality measure</option>

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diff changeset

617 <option value="de" selected="True">Sequence duplication - exact only</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

618 <option value="da" selected="True">Sequence duplication - exact + 5'/3'</option>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

619 <option value="sc" selected="True">Sequence complexity</option>

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diff changeset

620 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>

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parents:

diff changeset

621 </param>-->

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diff changeset

622 </inputs>

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diff changeset

623

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diff changeset

624 <outputs>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

625 <data format="fastq" name="good_sequence_file"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

626 from_work_dir="tmp/good_sequences.fastq"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

627 label="${tool.name} on ${on_string}: Good sequences" >

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628 <filter>seq_type['seq_type_opt'] == "single"</filter>

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diff changeset

629 </data>

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diff changeset

630 <data format="fastq" name="rejected_sequence_file"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

631 from_work_dir="tmp/rejected_sequences.fastq"

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diff changeset

632 label="${tool.name} on ${on_string}: Rejected sequences" >

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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633 <filter>seq_type['seq_type_opt'] == "single"</filter>

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parents:

diff changeset

634 </data>

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diff changeset

635

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parents:

diff changeset

636 <data format="fastq" name="good_sequences_1_file"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

637 from_work_dir="tmp/good_sequences_1.fastq"

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parents:

diff changeset

638 label="${tool.name} on ${on_string}: Good sequences for R1" >

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diff changeset

639 <filter>seq_type['seq_type_opt'] == "paired"</filter>

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diff changeset

640 </data>

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diff changeset

641 <data format="fastq" name="good_sequences_1_singletons_file"

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parents:

diff changeset

642 from_work_dir="tmp/good_sequences_1_singletons.fastq"

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parents:

diff changeset

643 label="${tool.name} on ${on_string}: Good singleton sequences for R1" >

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diff changeset

644 <filter>seq_type['seq_type_opt'] == "paired"</filter>

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diff changeset

645 </data>

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diff changeset

646 <data format="fastq" name="rejected_sequence_1_file"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

647 from_work_dir="tmp/rejected_sequences_1.fastq"

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parents:

diff changeset

648 label="${tool.name} on ${on_string}: Rejected sequences for R1" >

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parents:

diff changeset

649 <filter>seq_type['seq_type_opt'] == "paired"</filter>

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parents:

diff changeset

650 </data>

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parents:

diff changeset

651 <data format="fastq" name="good_sequences_2_file"

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diff changeset

652 from_work_dir="tmp/good_sequences_2.fastq"

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diff changeset

653 label="${tool.name} on ${on_string}: Good sequences for R2" >

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654 <filter>seq_type['seq_type_opt'] == "paired"</filter>

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iuc

parents:

diff changeset

655 </data>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

656 <data format="fastq" name="good_sequences_2_singletons_file"

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iuc

parents:

diff changeset

657 from_work_dir="tmp/good_sequences_2_singletons.fastq"

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diff changeset

658 label="${tool.name} on ${on_string}: Good singleton sequences for R2" >

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

659 <filter>seq_type['seq_type_opt'] == "paired"</filter>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

660 </data>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

661 <data format="fastq" name="rejected_sequence_2_file"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

662 from_work_dir="tmp/rejected_sequences_2.fastq"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

663 label="${tool.name} on ${on_string}: Rejected sequences for R2" >

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iuc

parents:

diff changeset

664 <filter>seq_type['seq_type_opt'] == "paired"</filter>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

665 </data>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

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diff changeset

666

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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667 <!--<data format="html" name="html_file"

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diff changeset

668 from_work_dir="stats_html.html"

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

669 label="${tool.name} on ${on_string}: Summary" />-->

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

670 </outputs>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

671

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

672 <tests>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

673 <test>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

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diff changeset

674 <param name='seq_type_opt' value="single"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

675 <param name="input_singles" value="prinseq_input_sequences.fastq"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

676 <param name='apply_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

677 <param name='apply_length_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

678 <param name='apply_min_length_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

679 <param name="min_length_filter_treatment_value" value="60"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

680 <param name='apply_max_length_filter_treatments' value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

681 <param name='apply_quality_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

682 <param name='apply_min_quality_filter_treatments' value="false" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

683 <param name='apply_max_quality_filter_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

684 <param name='apply_mean_quality_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

685 <param name='apply_min_mean_quality_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

686 <param name="min_mean_quality_filter_treatment_value" value="15"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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687 <param name='apply_max_mean_quality_filter_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

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688 <param name='apply_base_content_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

689 <param name='apply_GC_perc_content_filter_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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690 <param name='apply_N_number_content_filter_treatments' value="false"/>

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diff changeset

691 <param name='apply_N_percentage_content_filter_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

692 <param name="N_percentage_content_filter_treatment_value" value="2"/>

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693 <param name='apply_other_base_content_filter_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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694 <param name='apply_complexity_filter_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

695 <param name='apply_trimming_treatments' value="true" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

696 <param name='apply_length_trimming_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

697 <param name='apply_position_trimming_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

698 <param name='apply_tail_trimming_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

699 <param name='apply_quality_trimming_treatments' value="true"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

700 <param name='apply_left_quality_trimming_treatments' value="false"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

701 <param name='apply_right_quality_trimming_treatments' value="true" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

702 <param name="right_quality_trimming_treatment_value" value="20"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

703 <param name="type_quality_trimming_treatments" value="min"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

704 <param name="rule_quality_trimming_treatments" value="lt" />

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

705 <param name="window_quality_trimming_treatments" value="1"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

706 <param name="step_quality_trimming_treatments" value="1"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

707

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

708 <output name="good_sequence_file" file="prinseq_good_sequences.fastq"/>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

709 </test>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

710 </tests>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

711

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iuc

parents:

diff changeset

712 <help><![CDATA[

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

713

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

714 **What it does**

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

715

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

716 PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

717 This tool allow to process the sequences with filtering and trimming.

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

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diff changeset

718 More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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diff changeset

719

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

720 -----

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

721

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

722 **Input**

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

723

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

724 The input file is sequence file in fastq format (sequences and quality)::

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

725

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

726 @HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

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diff changeset

727 GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

728 +

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

729 CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

730

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

731 -----

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

732

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

733 **Parameters**

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

734

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

735 The parameters are numerous in PRINSEQ given the wanted treatments.

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

736

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

737 Several filter treatments are proposed:

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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parents:

diff changeset

738

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

739 - Filters based on sequence length

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

740 - Filters based on quality score

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

741 - Filters based on base content

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

iuc

parents:

diff changeset

742

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743 And several trimming treatments eliminate sequence parts:

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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744

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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745 - Trim of ends

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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746 - Trim of tails

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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747 - Trim based quality score

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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748

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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749 All these treaments can be customed using proposed parameters.

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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750

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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751 -----

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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752

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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753 **Output**

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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754

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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755 The output file is a sequence file with sequences and quality from input file

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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756 which have undergone filter and trimming.

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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757

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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758 ]]>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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759 </help>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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760

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761 <citations>

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762 <citation type="doi">10.1093/bioinformatics/btr026</citation>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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763 </citations>

ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1

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764 </tool>

Mercurial > repos > iuc > prinseq

annotate prinseq.xml @ 0:ba78b984a9eb draft