prinseq: prinseq.xml annotate

annotate prinseq.xml @ 3:02befcb391f5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070

author	iuc
date	Mon, 15 May 2017 11:03:57 -0400
parents	74afc47f326c
children	654b3a274ed5

rev	line source
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	1 <tool id="prinseq" name="PRINSEQ" version="0.20.4">
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 <requirements>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	4 <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	5 </requirements>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	6
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	7 <stdio>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	8 <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	9 <regex match="ERROR"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	10 source="stderr"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	11 level="fatal"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	12 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="WARNING"
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="warning"
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 </stdio>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	18
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	19 <version_command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	20 <![CDATA[
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	21 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	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
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	25 <command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	26 <![CDATA[
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	27 mkdir tmp/
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 &&
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	30
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	31 prinseq-lite.pl
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	32 #if $seq_type.seq_type_opt == "single":
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	33 -fastq '$seq_type.input_singles'
1 6b865dde1baa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit af00d26844b62927fd13703cd58ea3c59cc8f708 iuc parents: 0 diff changeset	34 #if $seq_type.input_singles.is_of_type('fastqillumina'):
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	35 -phred64
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	36 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	37 #else:
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	38 -fastq '$seq_type.input_mate1'
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	39 -fastq2 '$seq_type.input_mate2'
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	40 #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	41 #import sys
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	42 #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	43 #end if
1 6b865dde1baa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit af00d26844b62927fd13703cd58ea3c59cc8f708 iuc parents: 0 diff changeset	44 #if $seq_type.input_mate1.is_of_type('fastqillumina'):
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	45 -phred64
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	46 #end if
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
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	49 -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	50 -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	51
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	52 #if $filter_treatments.apply_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	53 #set length_filter_treatments=$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	54 #if $length_filter_treatments.apply_length_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	55 #set min_length_filter_treatments=$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	56 #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	57 -min_len $min_length_filter_treatments.min_length_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	58 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	59
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	60 #set max_length_filter_treatments=$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	61 #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	62 -max_len $max_length_filter_treatments.max_length_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	63 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	64 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	65
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	66 #set quality_filter_treatments=$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	67 #if $quality_filter_treatments.apply_quality_filter_treatments == "true":
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	68 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	69 #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	70 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	71 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	72
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	73 #set max_quality_filter_treatments=$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	74 #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	75 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	76 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	77
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	78 #set mean_quality_filter_treatments=$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	79 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	80 #set min_mean_quality_filter_treatments=$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	81 #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	82 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	83 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	84
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	85 #set max_mean_quality_filter_treatments=$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	86 #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	87 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	88 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	89 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	90 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	91
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	92 #set base_content_filter_treatments=$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	93 #if $base_content_filter_treatments.apply_base_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	94 #set GC_perc_content_filter_treatments=$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	95 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	96 #set min_GC_perc_content_filter_treatments=$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	97 #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	98 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	99 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	100
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	101 #set max_GC_perc_content_filter_treatments=$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	102 #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	103 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	104 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	105 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	106
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	107 #set N_number_content_filter_treatments=$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	108 #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	109 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	110 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	111
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	112 #set N_percentage_content_filter_treatments=$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	113 #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	114 -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	115 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	116
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	117 $base_content_filter_treatments.apply_other_base_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	118 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	119
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	120 #set complexity_filter_treatments=$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	121 #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	122 -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	123 -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	124 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	125
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	126 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	127
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	128 #if $trimming_treatments.apply_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	129 #set length_trimming_treatments=$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	130 #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	131 -trim_to_len $length_trimming_treatments.length_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	132 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	133
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	134 #set position_trimming_treatments=$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	135 #if $position_trimming_treatments.apply_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	136 #set nb_position_trimming_treatments=$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	137 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	138 #set left_position_trimming_treatments=$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	139 #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	140 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	141 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	142
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	143 #set right_position_trimming_treatments=$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	144 #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	145 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	146 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	147 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	148
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	149 #set percentage_position_trimming_treatments=$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	150 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	151 #set left_percentage_position_trimming_treatments=$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	152 #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	153 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	154 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	155
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	156 #set right_percentage_position_trimming_treatments=$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	157 #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	158 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	159 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	160 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	161 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	162
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	163 #set tail_trimming_treatments=$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	164 #if $tail_trimming_treatments.apply_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	165 #set a_t_tail_trimming_treatments=$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	166 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	167 #set left_a_t_tail_trimming_treatments=$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	168 #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	169 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	170 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	171
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	172 #set right_a_t_tail_trimming_treatments=$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	173 #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	174 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	175 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	176 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	177
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	178 #set ns_tail_trimming_treatments=$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	179 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	180 #set left_ns_tail_trimming_treatments=$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	181 #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	182 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	183 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	184
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	185 #set right_ns_tail_trimming_treatments=$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	186 #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	187 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	188 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	189 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	190 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	191
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	192 #set quality_trimming_treatments=$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	193 #if $quality_trimming_treatments.apply_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	194 #set left_quality_trimming_treatments=$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	195 #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	196 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	197 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	198
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	199 #set right_quality_trimming_treatments=$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	200 #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	201 -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	202 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	203
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	204 -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	205 -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	206 -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	207 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	208 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	209
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	210 #end if
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	211
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	212 #*
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	213 -graph_stats "$graph_stats"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	214 -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	215
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	216 &&
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	217
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	218 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	219 *#
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	220 ]]>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	221 </command>
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 <inputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	224 <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	225 <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	226 <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	227 <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	228 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	229 <when value="single">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	230 <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	231 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	232 <when value="paired">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	233 <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	234 <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	235 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	236 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	237
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	238 <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	239 <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	240 <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	241 <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	242 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	243 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	244 <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	245 <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	246 <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	247 <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	248 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	249 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	250 <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	251 <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	252 <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	253 <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	254 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	255 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	256 <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	257 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	258 <when value="false" />
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	259 </conditional>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	260 <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	261 <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	262 <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	263 <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	264 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	265 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	266 <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	267 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	268 <when value="false" />
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	269 </conditional>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	270 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	271 <when value="false" />
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	272 </conditional>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	273 <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	274 <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	275 <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	276 <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	277 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	278 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	279 <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	280 <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	281 <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	282 <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	283 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	284 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	285 <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	286 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	287 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	288 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	289 <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	290 <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	291 <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	292 <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	293 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	294 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	295 <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	296 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	297 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	298 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	299 <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	300 <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	301 <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	302 <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	303 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	304 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	305 <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	306 <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	307 <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	308 <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	309 </param>
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	310 <when value="true">
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	311 <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	312 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	313 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	314 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	315 <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	316 <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	317 <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	318 <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	319 </param>
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	320 <when value="true">
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	321 <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	322 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	323 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	324 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	325 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	326 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	327 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	328 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	329 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	330 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	331 <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	332 <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	333 <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	334 <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	335 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	336 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	337 <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	338 <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	339 <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	340 <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	341 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	342 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	343 <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	344 <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	345 <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	346 <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	347 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	348 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	349 <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	350 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	351 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	352 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	353 <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	354 <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	355 <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	356 <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	357 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	358 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	359 <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	360 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	361 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	362 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	363 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	364 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	365 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	366 <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	367 <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	368 <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	369 <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	370 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	371 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	372 <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	373 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	374 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	375 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	376 <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	377 <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	378 <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	379 <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	380 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	381 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	382 <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	383 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	384 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	385 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	386 <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	387 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	388 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	389 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	390 <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	391 <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	392 <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	393 <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	394 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	395 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	396 <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	397 <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	398 <option value="entropy" >Entropy</option>
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	399 </param>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	400 <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	401 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	402 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	403 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	404 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	405 <when value="false" />
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	406 </conditional>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	407
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	408 <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	409 <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	410 <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	411 <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	412 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	413 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	414 <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	415 <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	416 <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	417 <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	418 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	419 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	420 <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	421 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	422 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	423 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	424 <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	425 <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	426 <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	427 <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	428 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	429 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	430 <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	431 <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	432 <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	433 <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	434 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	435 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	436 <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	437 <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	438 <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	439 <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	440 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	441 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	442 <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	443 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	444 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	445 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	446 <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	447 <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	448 <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	449 <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	450 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	451 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	452 <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	453 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	454 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	455 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	456 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	457 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	458 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	459 <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	460 <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	461 <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	462 <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	463 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	464 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	465 <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	466 <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	467 <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	468 <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	469 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	470 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	471 <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	472 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	473 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	474 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	475 <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	476 <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	477 <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	478 <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	479 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	480 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	481 <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	482 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	483 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	484 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	485 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	486 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	487 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	488 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	489 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	490 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	491 <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	492 <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	493 <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	494 <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	495 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	496 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	497 <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	498 <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	499 <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	500 <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	501 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	502 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	503 <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	504 <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	505 <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	506 <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	507 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	508 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	509 <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	510 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	511 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	512 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	513 <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	514 <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	515 <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	516 <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	517 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	518 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	519 <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	520 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	521 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	522 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	523 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	524 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	525 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	526 <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	527 <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	528 <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	529 <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	530 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	531 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	532 <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	533 <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	534 <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	535 <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	536 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	537 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	538 <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	539 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	540 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	541 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	542 <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	543 <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	544 <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	545 <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	546 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	547 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	548 <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	549 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	550 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	551 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	552 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	553 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	554 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	555 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	556 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	557 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	558 <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	559 <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	560 <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	561 <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	562 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	563 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	564 <conditional name="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	565 <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	566 <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	567 <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	568 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	569 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	570 <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	571 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	572 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	573 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	574 <conditional name="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	575 <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 iuc parents: diff changeset	576 <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	577 <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	578 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	579 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	580 <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	581 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	582 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	583 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	584 <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	585 <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	586 <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	587 <option value="max" >Max</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	588 <option value="sum" >Sum</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	589 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	590 <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	591 <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	592 <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	593 <option value="et" >Equal to</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc 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="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	596 <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 iuc parents: diff changeset	597 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	598 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	599 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	600 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	601 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	602 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	603
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	604 <!--<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 iuc parents: diff changeset	605 <option value="ld" selected="True">Length distribution</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	606 <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 iuc parents: diff changeset	607 <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 iuc parents: diff changeset	608 <option value="ns" selected="True">Occurence of N</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	609 <option value="pt" selected="True">Poly-A/T tails</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	610 <option value="ts" selected="True">Tag sequence check</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	611 <option value="aq" selected="True">Assembly quality measure</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	612 <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 iuc parents: diff changeset	613 <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 iuc parents: diff changeset	614 <option value="sc" selected="True">Sequence complexity</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	615 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	616 </param>-->
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	617 </inputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	618
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	619 <outputs>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	620 <data format_source="input_singles" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	621 label="${tool.name} on ${on_string}: Good sequences" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	622 <filter>seq_type['seq_type_opt'] == "single"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	623 </data>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	624 <data format_source="input_singles" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	625 label="${tool.name} on ${on_string}: Rejected sequences" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	626 <filter>seq_type['seq_type_opt'] == "single"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	627 </data>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	628
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	629 <data format_source="input_mate1" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	630 label="${tool.name} on ${on_string}: Good sequences for R1" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	631 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	632 </data>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	633 <data format_source="input_mate1" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	634 label="${tool.name} on ${on_string}: Good singleton sequences for R1" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	635 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	636 </data>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	637 <data format_source="input_mate1" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	638 label="${tool.name} on ${on_string}: Rejected sequences for R1" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	639 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	640 </data>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	641 <data format_source="input_mate2" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	642 label="${tool.name} on ${on_string}: Good sequences for R2" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	643 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	644 </data>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	645 <data format_source="input_mate2" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	646 label="${tool.name} on ${on_string}: Good singleton sequences for R2" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	647 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	648 </data>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	649 <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	650 label="${tool.name} on ${on_string}: Rejected sequences for R2" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	651 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	652 </data>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	653
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	654 <!--<data format="html" name="html_file" from_work_dir="stats_html.html"
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	655 label="${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	656 </outputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	657
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	658 <tests>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	659 <test>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	660 <param name='seq_type_opt' value="single"/>
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	661 <param name="input_singles" value="prinseq_input_sequences.fastq" ftype="fastqsanger"/>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	662 <param name='apply_filter_treatments' value="true"/>
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	663 <param name='apply_length_filter_treatments' value="true"/>
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	664 <param name='apply_min_length_filter_treatments' value="true"/>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	665 <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	666 <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 iuc parents: diff changeset	667 <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 iuc parents: diff changeset	668 <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 iuc parents: diff changeset	669 <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 iuc parents: diff changeset	670 <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 iuc parents: diff changeset	671 <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	672 <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 iuc parents: diff changeset	673 <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 iuc parents: diff changeset	674 <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 iuc parents: diff changeset	675 <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 iuc parents: diff changeset	676 <param name='apply_N_number_content_filter_treatments' value="false"/>
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	677 <param name='apply_N_percentage_content_filter_treatments' value="true"/>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	678 <param name="N_percentage_content_filter_treatment_value" value="2"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	679 <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 iuc parents: diff changeset	680 <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 iuc parents: diff changeset	681 <param name='apply_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	682 <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 iuc parents: diff changeset	683 <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 iuc parents: diff changeset	684 <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 iuc parents: diff changeset	685 <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 iuc parents: diff changeset	686 <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 iuc parents: diff changeset	687 <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	688 <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	689 <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	690 <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	691 <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	692 <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 iuc parents: diff changeset	693
3 02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070 iuc parents: 2 diff changeset	694 <output name="good_sequence_file" file="prinseq_good_sequences.fastq" ftype="fastqsanger"/>
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	695 </test>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	696 </tests>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	697
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	698 <help><![CDATA[
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	699 What it does
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	700
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	701 PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	702 This tool allow to process the sequences with filtering and trimming.
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	703 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 iuc parents: diff changeset	704
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	705 -----
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	706
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	707 Input
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	708
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	709 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	710
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	711 @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 parents: diff changeset	712 GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	713 +
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	714 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	715
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	716 -----
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	717
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	718 Parameters
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: 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 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	721
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	722 Several filter treatments are proposed:
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	723
2 74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b iuc parents: 1 diff changeset	724 - Filters based on sequence length
0 ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	725 - 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	726 - 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	727
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	728 And several trimming treatments eliminate sequence parts:
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	729
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	730 - Trim of ends
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	731 - Trim of tails
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	732 - Trim based quality score
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	733
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	734 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 iuc parents: diff changeset	735
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
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	738 Output
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	739
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	740 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 iuc parents: diff changeset	741 which have undergone filter and trimming.
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	742 ]]>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	743 </help>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	744
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	745 <citations>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	746 <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 iuc parents: diff changeset	747 </citations>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: diff changeset	748 </tool>

Mercurial > repos > iuc > prinseq

annotate prinseq.xml @ 3:02befcb391f5 draft