prinseq: prinseq.xml annotate

annotate prinseq.xml @ 3:10ac5c567b73 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d

author	bebatut
date	Tue, 17 Nov 2015 06:02:09 -0500
parents	6912790a4287
children	acaf871de2ea

rev	line source
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	1 <tool id="prinseq" name="PRINSEQ" version="0.1.0">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	2 <description>to process quality of sequences</description>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	3
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	4 <requirements>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	5 <requirement type="package" version="0.20.4">prinseq</requirement>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	6 </requirements>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	7
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	8 <stdio>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	9 <exit_code range="1:" level="fatal" description="" />
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	10 <regex match="ERROR"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	11 source="stderr"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	12 level="fatal"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	13 description="" />
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	14 <regex match="WARNING"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	15 source="stderr"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	16 level="warning"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	17 description="" />
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	18 </stdio>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	19
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	20 <version_command>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	21 <![CDATA[
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	22 perl \${PRINSEQ_DIR}/prinseq-lite.pl --version
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	23 ]]>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	24 </version_command>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	25
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	26 <command>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	27 <![CDATA[
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	28 perl \${PRINSEQ_DIR}/prinseq-lite.pl
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	29 -fastq $sequence_to_control_file
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	30 -out_good good_sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	31 -out_bad rejected_sequences
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	32
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	33 #if $filter_treatments.apply_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	34 #set length_filter_treatments=$filter_treatments.length_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	35 #if $length_filter_treatments.apply_length_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	36 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	37 #if $min_length_filter_treatments.apply_min_length_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	38 -min_len $min_length_filter_treatments.min_length_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	39 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	40 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	41 #if $max_length_filter_treatments.apply_max_length_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	42 -max_len $max_length_filter_treatments.max_length_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	43 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	44 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	45
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	46 #set quality_filter_treatments=$filter_treatments.quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	47 #if $quality_filter_treatments.apply_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	48 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	49 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	50 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	51 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	52 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	53 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	54 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	55 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	56 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	57 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	58 #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	59 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments:
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	60 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	61 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	62 #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	63 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments:
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	64 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	65 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	66 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	67 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	68
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	69 #set base_content_filter_treatments=$filter_treatments.base_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	70 #if $base_content_filter_treatments.apply_base_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	71 #set GC_perc_content_filter_treatments=$base_content_filter_treatments.GC_perc_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	72 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	73 #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	74 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	75 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	76 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	77 set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	78 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	79 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	80 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	81 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	82 #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	83 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	84 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	85 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	86 #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	87 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	88 -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	89 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	90 #if $base_content_filter_treatments.apply_other_base_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	91 -noniupac
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	92 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	93 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	94
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	95 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	96 #if $complexity_filter_treatments.apply_complexity_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	97 -lc_method $complexity_filter_treatments.method_complexity_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	98 -lc_threshold $complexity_filter_treatments.threshold_complexity_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	99 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	100
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	101 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	102
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	103 #if $trimming_treatments.apply_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	104 #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	105 #if $length_trimming_treatments.apply_length_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	106 -trim_to_len $length_trimming_treatments.length_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	107 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	108
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	109 #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	110 #if $position_trimming_treatments.apply_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	111 #set nb_position_trimming_treatments=$position_trimming_treatments.nb_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	112 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	113 #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	114 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	115 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	116 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	117 #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	118 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	119 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	120 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	121 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	122 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	123 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	124 #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	125 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	126 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	127 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	128 #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	129 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	130 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	131 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	132 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	133 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	134
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	135 #set tail_trimming_treatments=$trimming_treatments.tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	136 #if $tail_trimming_treatments.apply_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	137 #set a_t_tail_trimming_treatments=$tail_trimming_treatments.a_t_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	138 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	139 #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	140 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	141 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	142 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	143 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	144 #if right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	145 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	146 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	147 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	148 #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	149 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	150 #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	151 #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	152 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	153 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	154 #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	155 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	156 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	157 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	158 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	159 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	160
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	161 #set quality_trimming_treatments=$trimming_treatments.quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	162 #if $quality_trimming_treatments.apply_quality_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	163 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	164 #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	165 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	166 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	167 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	168 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments :
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	169 -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	170 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	171 -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	172 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	173 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	174 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	175 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	176
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	177 #end if
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	178 ]]>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	179 </command>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	180
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	181 <inputs>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	182 <param name="sequence_to_control_file" type="data" format="fastq" label="Input
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	183 sequence file" help="The file must be in fastq format for quality
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	184 scores"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	185
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	186 <conditional name="filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	187 <param name='apply_filter_treatments' type='boolean' checked="true"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	188 label="Apply filter treatments?" help=""/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	189 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	190 <conditional name="length_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	191 <param name='apply_length_filter_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	192 checked="true" label="Filter sequence based on their
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	193 length?" help="By default, sequences smaller than 60 bp
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	194 are removed. No top threshold is defined"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	195 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	196 <conditional name="min_length_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	197 <param name='apply_min_length_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	198 type='boolean' checked="true" label="Filter too
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	199 small sequences?" help="By default, sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	200 smaller than 60 bp are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	201 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	202 <param name="min_length_filter_treatment_value" type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	203 max="3000" value="60" label="Minimum length t
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	204 hreshold to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	205 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	206 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	207 <conditional name="max_length_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	208 <param name='apply_max_length_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	209 type='boolean' checked="false" label="Filter too
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	210 big sequences?" help="By default, no treatment
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	211 based on a maximal length is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	212 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	213 <param name="max_length_filter_treatment_value" type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	214 max="3000" value="1000" label="Maximal length
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	215 threshold to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	216 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	217 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	218 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	219 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	220 <conditional name="quality_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	221 <param name='apply_quality_filter_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	222 checked="true" label="Filter sequences based on quality
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	223 score?" help="By default, sequences with a mean score
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	224 below 15 are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	225 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	226 <conditional name="min_quality_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	227 <param name='apply_min_quality_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	228 type='boolean' checked="false" label="Filter sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	229 based on their minimum score?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	230 no treatment based on a minimum score is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	231 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	232 <param name="min_quality_filter_treatment_value" type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	233 max="40" value="2" label="Minimum score threshold
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	234 to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	235 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	236 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	237 <conditional name="max_quality_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	238 <param name='apply_max_quality_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	239 type='boolean' checked="false" label="Filter sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	240 based on their maximum score?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	241 no treatment based on a maximum score is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	242 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	243 <param name="max_quality_filter_treatment_value" type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	244 max="40" value="38" label="Maximum score
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	245 threshold to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	246 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	247 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	248 <conditional name="mean_quality_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	249 <param name='apply_mean_quality_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	250 type='boolean' checked="true" label="Filter sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	251 based on their mean score?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	252 sequences with a mean score below 15 are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	253 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	254 <conditional name="min_mean_quality_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	255 <param name='apply_min_mean_quality_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	256 type='boolean' checked="true" label="Filter
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	257 sequences with too small mean score?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	258 help="By default, sequences with a mean
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	259 score below 15 are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	260 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	261 <param name="min_mean_quality_filter_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	262 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	263 max="40" value="15" label="Minimum mean
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	264 score threshold to conserve sequences"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	265 help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	266 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	267 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	268 <conditional name="max_mean_quality_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	269 <param name='apply_max_mean_quality_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	270 type='boolean' checked="false" label="Filter
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	271 sequences with too high mean score?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	272 help="By default, no treatment based on
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	273 a maximum mean score is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	274 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	275 <param name="max_mean_quality_filter_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	276 type="integer"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	277 min="0" max="40" value="40"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	278 label="Maximum mean score threshold
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	279 to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	280 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	281 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	282 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	283 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	284 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	285 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	286 <conditional name="base_content_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	287 <param name='apply_base_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	288 type='boolean' checked="true" label="Filter sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	289 based on their base content?" help="By default, sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	290 with more than 2% of N bases are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	291 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	292 <conditional name="GC_perc_content_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	293 <param name='apply_GC_perc_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	294 type='boolean' checked="false" label="Filter
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	295 sequences based on their GC percentage?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	296 help="By default, no treatment based on GC percentage
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	297 is made."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	298 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	299 <conditional name="min_GC_perc_content_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	300 <param name='apply_min_GC_perc_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	301 type='boolean' checked="false" label="Filter
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	302 sequences with too small GC percentage?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	303 help="By default, no treatment based on
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	304 GC percentage is made."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	305 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	306 <param name="min_GC_perc_content_filter_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	307 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	308 max="100" value="10" label="Minimal
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	309 GC percentage threshold to conserve
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	310 sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	311 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	312 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	313 <conditional name="max_GC_perc_content_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	314 <param name='apply_max_GC_perc_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	315 type='boolean' checked="false" label="Filter
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	316 sequences with too high GC percentage?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	317 help="By default, no treatment based on
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	318 GC percentage is made."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	319 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	320 <param name="max_GC_perc_content_filter_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	321 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	322 max="100" value="90" label="Maximal GC
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	323 percentage threshold to conserve
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	324 sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	325 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	326 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	327 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	328 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	329 <conditional name="N_number_content_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	330 <param name='apply_N_number_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	331 type='boolean' checked="false" label="Filter
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	332 sequences based on their number of N bases?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	333 help="By default, no treatment based on N number
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	334 is made."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	335 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	336 <param name="N_number_content_filter_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	337 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	338 max="3000" value="10" label="Maximal N number
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	339 threshold to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	340 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	341 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	342 <conditional name="N_percentage_content_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	343 <param name='apply_N_percentage_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	344 type='boolean' checked="true" label="Filter sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	345 based on their percentage of N bases?" help="By
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	346 default, sequences with more than 2% of N bases
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	347 are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	348 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	349 <param name="N_percentage_content_filter_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	350 type="integer" min="0" max="100"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	351 value="2" label="Maximal N percentage threshold
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	352 to conserve sequences" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	353 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	354 </conditional>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	355 <param name='apply_other_base_content_filter_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	356 type='boolean' checked="false" label="Filter sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	357 with characters other than A, T, C, G and N?" help="By
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	358 default, this treatment is not made."/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	359 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	360 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	361 <conditional name="complexity_filter_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	362 <param name='apply_complexity_filter_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	363 checked="false" label="Filter sequences based on their
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	364 complexity?" help="By default, no complexity filter is
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	365 applied"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	366 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	367 <param name="method_complexity_filter_treatments" type="select"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	368 display="radio" label="Method to filter low complexity
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	369 sequences" help="">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	370 <option value="dust">Dust</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	371 <option value="entropy" >Entropy</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	372 </param>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	373 <param name="threshold_complexity_filter_treatments" type="integer"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	374 min="0" max="100" value="2" label="Threshold value used
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	375 to filter sequences by sequence complexity" help="The
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	376 dust method uses the threshold as maximum allowed score
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	377 and the entropy method as minimum allowed value."/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	378 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	379 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	380 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	381 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	382
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	383 <conditional name="trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	384 <param name='apply_trimming_treatments' type='boolean' checked="true"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	385 label="Apply trimming treatments?" help=""/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	386 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	387 <conditional name="length_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	388 <param name='apply_length_trimming_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	389 checked="false" label="Trim all sequences from the 3'-end
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	390 to a length?" help="By default, no length trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	391 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	392 <param name="length_trimming_treatment_value" type="integer" min="0" max="3000"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	393 value="100" label="Length of sequences after
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	394 trimming" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	395 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	396 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	397 <conditional name="position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	398 <param name='apply_position_trimming_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	399 checked="false" label="Trim all sequences from the ends?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	400 help="By default, no position trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	401 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	402 <conditional name="nb_position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	403 <param name='apply_nb_position_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	404 type='boolean' checked="false" label="Trim sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	405 by a defined number of positions?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	406 no position trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	407 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	408 <conditional name="left_position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	409 <param name='apply_left_position_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	410 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	411 sequences at the 5'-end by a defined number
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	412 of positions?" help="By default, no position
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	413 trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	414 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	415 <param name="left_position_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	416 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	417 max="3000" value="100" label="Number of
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	418 positions to trim on 5'-end" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	419 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	420 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	421 <conditional name="right_position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	422 <param name='apply_right_position_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	423 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	424 sequences at the 3'-end by a defined number
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	425 of positions?" help="By default, no position
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	426 trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	427 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	428 <param name="right_position_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	429 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	430 max="3000" value="100" label="Number
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	431 of positions to trim on 3'-end"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	432 help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	433 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	434 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	435 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	436 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	437 <conditional name="percentage_position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	438 <param name='apply_percentage_position_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	439 type='boolean' checked="false" label="Trim sequences
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	440 by a defined percentage of read length?" help="By
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	441 default, no position trimming is made. The trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	442 length is rounded towards the lower integer"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	443 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	444 <conditional name="left_percentage_position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	445 <param name='apply_left_percentage_position_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	446 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	447 sequences at the 5'-end by a defined percentage
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	448 of read length?" help="By default, no position
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	449 trimming is made. The trim length is rounded
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	450 towards the lower integer"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	451 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	452 <param name="left_percentage_position_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	453 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	454 max="100" value="2" label="Percentage
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	455 of positions to trim on 5'-end" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	456 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	457 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	458 <conditional name="right_percentage_position_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	459 <param name='apply_right_percentage_position_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	460 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	461 sequences at the 3'-end by a defined percentage
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	462 of read length?" help="By default, no position
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	463 trimming is made. The trim length is rounded
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	464 towards the lower integer"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	465 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	466 <param name="right_percentage_position_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	467 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	468 max="100" value="2" label="Percentage
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	469 of positions to trim on 3'-end" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	470 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	471 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	472 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	473 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	474 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	475 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	476 <conditional name="tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	477 <param name='apply_tail_trimming_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	478 checked="false" label="Trim tails?" help="By default, no
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	479 tail trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	480 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	481 <conditional name="a_t_tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	482 <param name='apply_a_t_tail_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	483 type='boolean' checked="false" label="Trim poly-A/T
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	484 tail?" help="By default, no poly-A/T tail trimming
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	485 is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	486 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	487 <conditional name="left_a_t_tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	488 <param name='apply_left_a_t_tail_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	489 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	490 poly-A/T tail at the 5'-end?" help="By
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	491 default, no 5'-end poly-A/T tail trimming
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	492 is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	493 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	494 <param name="left_a_t_tail_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	495 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	496 max="3000" value="100" label="Minimum
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	497 length of poly-A/T to trim at the 5'-end"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	498 help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	499 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	500 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	501 <conditional name="right_a_t_tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	502 <param name='apply_right_a_t_tail_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	503 type='boolean' checked="false" label="Trim poly-A/T
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	504 tail at the 5'-end?" help="By default, no
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	505 3'-end poly-A/T tail trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	506 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	507 <param name="right_a_t_tail_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	508 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	509 max="3000" value="100" label="Minimum
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	510 length of poly-A/T to trim at the 5'-end"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	511 help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	512 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	513 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	514 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	515 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	516 <conditional name="ns_tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	517 <param name='apply_ns_tail_trimming_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	518 checked="false" label="Trim poly-N tail?" help="By
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	519 default, no poly-N tail trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	520 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	521 <conditional name="left_ns_tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	522 <param name='apply_left_ns_tail_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	523 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	524 poly-N tail at the 5'-end?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	525 no 5'-end poly-N tail trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	526 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	527 <param name="left_ns_tail_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	528 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	529 max="3000" value="100" label="Minimum
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	530 length of poly-N to trim at the 5'-end"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	531 help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	532 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	533 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	534 <conditional name="right_ns_tail_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	535 <param name='apply_right_ns_tail_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	536 type='boolean' checked="false" label="Trim
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	537 poly-N tail at the 5'-end?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	538 no 3'-end poly-N tail trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	539 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	540 <param name="right_ns_tail_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	541 type="integer" min="0"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	542 max="3000" value="100" label="Minimum
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	543 length of poly-N to trim at the 5'-end"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	544 help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	545 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	546 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	547 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	548 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	549 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	550 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	551 <conditional name="quality_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	552 <param name='apply_quality_trimming_treatments' type='boolean'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	553 checked="true" label="Trim sequence by quality score?"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	554 help="By default, a 3'-end trimming is made to remove ends
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	555 with a minimum quality score over 5 bp below 20"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	556 <when value="true">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	557 <conditional name="left_quality_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	558 <param name='apply_left_quality_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	559 type='boolean' checked="false" label="Trim sequence
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	560 by quality score from the 5'-end?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	561 no 5'-end quality trimming is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	562 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	563 <param name="left_quality_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	564 type="integer" min="0" max="40"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	565 value="20" label="Quality score threshold to
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	566 trim positions" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	567 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	568 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	569 <conditional name="right_quality_trimming_treatments">
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	570 <param name='apply_right_quality_trimming_treatments'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	571 type='boolean' checked="true" label="Trim sequence
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	572 by quality score from the 3'-end?" help="By default,
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	573 3'-end trimming is made based on a score of 20"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	574 <when value="true">
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	575 <param name="right_quality_trimming_treatment_value"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	576 type="integer" min="0" max="40"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	577 value="20" label="Quality score threshold to
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	578 trim positions" help=""/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	579 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	580 </conditional>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	581 <param name="type_quality_trimming_treatments" type="select"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	582 display="radio" label="Type of quality score calculation
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	583 to use" help="By default, min is used">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	584 <option value="min" selected="true">Mininum</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	585 <option value="mean" >Mean</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	586 <option value="max" >Max</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	587 <option value="sum" >Sum</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	588 </param>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	589 <param name="rule_quality_trimming_treatments" type="select"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	590 display="radio" label="Rule tu use to compare quality
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	591 score to calculated value" help="By default, 'less than'
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	592 is used">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	593 <option value="lt" selected="true">Less than</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	594 <option value="gt" >Greater than</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	595 <option value="et" >Equal to</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	596 </param>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	597 <param name="window_quality_trimming_treatments" type="integer"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	598 min="0" max="300" value="1" label="Size of the sliding
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	599 window used to calculated quality score by type" help="To
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	600 stop at the first base that fails the rule defined, use a
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	601 window size of 1 (default value)"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	602 <param name="step_quality_trimming_treatments" type="integer"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	603 min="0" max="300" value="1" label="Step size used to move
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	604 the sliding window" help="To move the window over all
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	605 quality scores without missing any, the step size sould
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	606 be less or equal to the window size. The default value
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	607 is 1."/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	608 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	609 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	610 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	611 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	612 </inputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	613
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	614 <outputs>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	615 <data format="fastq" name="good_sequence_file"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	616 from_work_dir="good_sequences.fastq"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	617 label="Good sequences of ${on_string} (PRINSEQ)" />
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	618 <data format="fastq" name="rejected_sequence_file"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	619 from_work_dir="rejected_sequences.fastq"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	620 label="Rejected sequences of ${on_string} (PRINSEQ)" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	621 </outputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	622
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	623 <tests>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	624 <test>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	625 <param name="sequence_to_control_file" value="prinseq_input_sequences.fastq"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	626 <param name='apply_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	627 <param name='apply_length_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	628 <param name='apply_min_length_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	629 <param name="min_length_filter_treatment_value" value="60"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	630 <param name='apply_max_length_filter_treatments' value="false" />
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	631 <param name='apply_quality_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	632 <param name='apply_min_quality_filter_treatments' value="false" />
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	633 <param name='apply_max_quality_filter_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	634 <param name='apply_mean_quality_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	635 <param name='apply_min_mean_quality_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	636 <param name="min_mean_quality_filter_treatment_value" value="15"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	637 <param name='apply_max_mean_quality_filter_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	638 <param name='apply_base_content_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	639 <param name='apply_GC_perc_content_filter_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	640 <param name='apply_N_number_content_filter_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	641 <param name='apply_N_percentage_content_filter_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	642 <param name="N_percentage_content_filter_treatment_value" value="2"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	643 <param name='apply_other_base_content_filter_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	644 <param name='apply_complexity_filter_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	645 <param name='apply_trimming_treatments' value="true" />
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	646 <param name='apply_length_trimming_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	647 <param name='apply_position_trimming_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	648 <param name='apply_tail_trimming_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	649 <param name='apply_quality_trimming_treatments' value="true"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	650 <param name='apply_left_quality_trimming_treatments' value="false"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	651 <param name='apply_right_quality_trimming_treatments' value="true" />
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	652 <param name="right_quality_trimming_treatment_value" value="20"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	653 <param name="type_quality_trimming_treatments" value="min"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	654 <param name="rule_quality_trimming_treatments" value="lt" />
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	655 <param name="window_quality_trimming_treatments" value="1"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	656 <param name="step_quality_trimming_treatments" value="1"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	657
3 10ac5c567b73 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d bebatut parents: 2 diff changeset	658 <output name="good_sequence_file" file="prinseq_good_sequences.fastq"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	659 </test>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	660 </tests>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	661
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	662 <help><![CDATA[
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	663
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	664 What it does
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	665
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	666 PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	667 This tool allow to process the sequences with filtering and trimming.
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	668 More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	669
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	670 -----
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	671
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	672 Input
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	673
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	674 The input file is sequence file in fastq format (sequences and quality)::
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	675
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	676 @HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	677 GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	678 +
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	679 CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	680
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	681 -----
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	682
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	683 Parameters
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	684
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	685 The parameters are numerous in PRINSEQ
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	686
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	687 - Filtering parameters to eliminate sequences
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	688 - Filters based on sequence length
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	689 - Filters based on quality score
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	690 - Filters based on base content
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	691 - Trimming parameters to eliminate sequence parts
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	692 - Trim of ends
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	693 - Trim of tails
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	694 - Trim based quality score
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	695
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	696 -----
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	697
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	698 Output
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	699
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	700 The output file is a sequence file with sequences and quality from input file
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	701 which have undergone filter and trimming.
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	702
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	703 ]]>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	704 </help>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	705
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	706 <citations>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	707 <citation type="doi">10.1093/bioinformatics/btr026</citation>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	708 </citations>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	709 </tool>

Mercurial > repos > bebatut > prinseq

annotate prinseq.xml @ 3:10ac5c567b73 draft