prinseq: prinseq.xml annotate

annotate prinseq.xml @ 4:acaf871de2ea draft default tip

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty

author	bebatut
date	Wed, 27 Jan 2016 03:55:09 -0500
parents	10ac5c567b73
children

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[
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	28 perl \${PRINSEQ_DIR}/prinseq-lite.pl
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	29 #if $seq_type.seq_type_opt == 'single':
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	30 -fastq "$seq_type.input_singles"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	31 #if $seq_type.input_singles.ext == 'fastqillumina':
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	32 -phred64
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	33 #end if
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	34 #else:
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	35 -fastq "$seq_type.input_mate1"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	36 -fastq2 "$seq_type.input_mate2"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	37 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	38 #import sys
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	39 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	40 #end if
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	41 #if $seq_type.input_mate1.ext == 'fastqillumina':
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	42 -phred64
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	43 #end if
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	44 #end if
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	45
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	46 -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	47 -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	48
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	49 #if $filter_treatments.apply_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	50 #set length_filter_treatments=$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	51 #if $length_filter_treatments.apply_length_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	52 #set min_length_filter_treatments=$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	53 #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	54 -min_len $min_length_filter_treatments.min_length_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	55 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	56
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	57 #set max_length_filter_treatments=$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	58 #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	59 -max_len $max_length_filter_treatments.max_length_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	60 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	61 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	62
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	63 #set quality_filter_treatments=$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	64 #if $quality_filter_treatments.apply_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	65 #set min_quality_filter_treatments=$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	66 #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	67 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	68 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	69
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	70 #set max_quality_filter_treatments=$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	71 #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	72 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	73 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	74
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	75 #set mean_quality_filter_treatments=$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	76 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	77 #set min_mean_quality_filter_treatments=$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	78 #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	79 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	80 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	81
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	82 #set max_mean_quality_filter_treatments=$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	83 #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	84 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	85 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	86 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	87 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	88
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	89 #set base_content_filter_treatments=$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	90 #if $base_content_filter_treatments.apply_base_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	91 #set GC_perc_content_filter_treatments=$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	92 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	93 #set min_GC_perc_content_filter_treatments=$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	94 #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	95 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	96 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	97
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	98 #set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	99 #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	100 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	101 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	102 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	103
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	104 #set N_number_content_filter_treatments=$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	105 #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	106 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	107 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	108
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	109 #set N_percentage_content_filter_treatments=$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	110 #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	111 -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	112 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	113
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	114 $base_content_filter_treatments.apply_other_base_content_filter_treatments
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	115 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	116
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	117 #set complexity_filter_treatments=$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	118 #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	119 -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	120 -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	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
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	123 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	124
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	125 #if $trimming_treatments.apply_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	126 #set length_trimming_treatments=$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	127 #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	128 -trim_to_len $length_trimming_treatments.length_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	129 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	130
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	131 #set position_trimming_treatments=$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	132 #if $position_trimming_treatments.apply_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	133 #set nb_position_trimming_treatments=$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	134 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	135 #set left_position_trimming_treatments=$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	136 #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	137 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	138 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	139
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	140 #set right_position_trimming_treatments=$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	141 #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	142 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	143 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	144 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	145
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	146 #set percentage_position_trimming_treatments=$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	147 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	148 #set left_percentage_position_trimming_treatments=$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	149 #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	150 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	151 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	152
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	153 #set right_percentage_position_trimming_treatments=$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	154 #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	155 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	156 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	157 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	158 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	159
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	160 #set tail_trimming_treatments=$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	161 #if $tail_trimming_treatments.apply_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	162 #set a_t_tail_trimming_treatments=$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	163 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	164 #set left_a_t_tail_trimming_treatments=$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	165 #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	166 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	167 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	168
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	169 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	170 #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	171 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	172 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	173 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	174
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	175 #set ns_tail_trimming_treatments=$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	176 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	177 #set left_ns_tail_trimming_treatments=$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	178 #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	179 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	180 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	181
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	182 #set right_ns_tail_trimming_treatments=$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	183 #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	184 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	185 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	186 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	187 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	188
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	189 #set quality_trimming_treatments=$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	190 #if $quality_trimming_treatments.apply_quality_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	191 #set left_quality_trimming_treatments=$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	192 #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	193 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	194 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	195
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	196 #set right_quality_trimming_treatments=$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	197 #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	198 -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	199 #end if
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	200
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	201 -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	202 -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	203 -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	204 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	205 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	206
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	207 #end if
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	208
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	209 -graph_stats "$graph_stats"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	210 -graph_data stats.gd
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	211 ;
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	212
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	213 # perl \${PRINSEQ_DIR}/prinseq-graphs-noPCA.pl -i stats.gd -html_all -o stats_html
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	214
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	215
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	216 ]]>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	217 </command>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	218
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	219 <inputs>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	220 <conditional name="seq_type">
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	221 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	222 <option value="single">Single-end</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	223 <option value="paired">Paired-end</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	224 </param>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	225 <when value="single">
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	226 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	227 </when>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	228 <when value="paired">
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	229 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	230 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	231 </when>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	232 </conditional>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	233
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	234 <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	235 <param name='apply_filter_treatments' type='boolean' checked="true"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	236 truevalue="true" falsevalue="false" label="Apply filter treatments?"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	237 help=""/>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	238 <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	239 <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	240 <param name='apply_length_filter_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	241 checked="true" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	242 label="Filter sequence based on their length?" help="By
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	243 default, sequences smaller than 60 bp
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	244 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	245 <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	246 <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	247 <param name='apply_min_length_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	248 type='boolean' checked="true" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	249 falsevalue="false" label="Filter too
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	250 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	251 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	252 <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	253 <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	254 max="3000" value="60" label="Minimum length t
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	255 hreshold to conserve sequences" help="(-min_len)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	256 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	257 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	258 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	259 <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	260 <param name='apply_max_length_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	261 type='boolean' truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	262 checked="false" label="Filter too
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	263 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	264 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	265 <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	266 <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	267 max="3000" value="1000" label="Maximal length
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	268 threshold to conserve sequences" help="(-max_len)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	269 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	270 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	271 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	272 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	273 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	274 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	275 <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	276 <param name='apply_quality_filter_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	277 checked="true" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	278 label="Filter sequences based on quality
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	279 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	280 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	281 <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	282 <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	283 <param name='apply_min_quality_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	284 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	285 falsevalue="false" label="Filter sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	286 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	287 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	288 <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	289 <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	290 max="40" value="2" label="Minimum score threshold
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	291 to conserve sequences" help="(-min_qual_score)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	292 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	293 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	294 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	295 <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	296 <param name='apply_max_quality_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	297 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	298 falsevalue="false" label="Filter sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	299 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	300 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	301 <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	302 <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	303 max="40" value="38" label="Maximum score
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	304 threshold to conserve sequences" help="(-max_qual_score)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	305 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	306 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	307 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	308 <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	309 <param name='apply_mean_quality_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	310 type='boolean' checked="true" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	311 falsevalue="false" label="Filter sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	312 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	313 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	314 <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	315 <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	316 <param name='apply_min_mean_quality_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	317 type='boolean' checked="true" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	318 falsevalue="false" label="Filter
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	319 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	320 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	321 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	322 <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	323 <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	324 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	325 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	326 score threshold to conserve sequences"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	327 help="(-min_qual_mean)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	328 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	329 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	330 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	331 <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	332 <param name='apply_max_mean_quality_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	333 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	334 falsevalue="false" label="Filter
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	335 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	336 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	337 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	338 <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	339 <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	340 type="integer"
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	341 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	342 label="Maximum mean score threshold
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	343 to conserve sequences" help="(-max_qual_mean)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	344 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	345 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	346 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	347 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	348 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	349 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	350 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	351 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	352 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	353 <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	354 <param name='apply_base_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	355 type='boolean' checked="true" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	356 label="Filter sequences based on their base content?"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	357 help="By default, sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	358 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	359 <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	360 <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	361 <param name='apply_GC_perc_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	362 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	363 falsevalue="false" label="Filter
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	364 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	365 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	366 is made."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	367 <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	368 <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	369 <param name='apply_min_GC_perc_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	370 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	371 falsevalue="false" label="Filter
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	372 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	373 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	374 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	375 <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	376 <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	377 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	378 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	379 GC percentage threshold to conserve
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	380 sequences" help="(-min_gc)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	381 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	382 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	383 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	384 <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	385 <param name='apply_max_GC_perc_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	386 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	387 falsevalue="false" label="Filter
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	388 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	389 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	390 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	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="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	393 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	394 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	395 percentage threshold to conserve
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	396 sequences" help="(-max_gc)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	397 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	398 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	399 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	400 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	401 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	402 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	403 <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	404 <param name='apply_N_number_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	405 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	406 falsevalue="false" label="Filter sequences based
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	407 on their number of N bases?"
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	408 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	409 is made."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	410 <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	411 <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	412 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	413 max="3000" value="10" label="Maximal N number
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	414 threshold to conserve sequences" help="(-ns_max_n)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	415 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	416 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	417 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	418 <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	419 <param name='apply_N_percentage_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	420 type='boolean' checked="true" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	421 falsevalue="false" label="Filter sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	422 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	423 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	424 are removed."/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	425 <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	426 <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	427 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	428 value="2" label="Maximal N percentage threshold
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	429 to conserve sequences" help="(-ns_max_p)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	430 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	431 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	432 </conditional>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	433 <param name='apply_other_base_content_filter_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	434 type='boolean' truevalue="-noniupac" falsevalue=""
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	435 checked="false" label="Filter sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	436 with characters other than A, T, C, G and N?" help="By
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	437 default, this treatment is not made. (-noniupac)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	438 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	439 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	440 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	441 <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	442 <param name='apply_complexity_filter_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	443 checked="false" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	444 label="Filter sequences based on their
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	445 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	446 applied"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	447 <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	448 <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	449 display="radio" label="Method to filter low complexity
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	450 sequences" help="(-lc_method)">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	451 <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	452 <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	453 </param>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	454 <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	455 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	456 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	457 dust method uses the threshold as maximum allowed score
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	458 and the entropy method as minimum allowed value.(-lc_threshold)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	459 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	460 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	461 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	462 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	463 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	464 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	465
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	466 <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	467 <param name='apply_trimming_treatments' type='boolean' checked="true"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	468 truevalue="true" falsevalue="false" label="Apply trimming
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	469 treatments?" help=""/>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	470 <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	471 <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	472 <param name='apply_length_trimming_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	473 checked="false" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	474 label="Trim all sequences from the 3'-end
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	475 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	476 <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	477 <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	478 value="100" label="Length of sequences after
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	479 trimming" help="(-trim_to_len)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	480 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	481 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	482 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	483 <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	484 <param name='apply_position_trimming_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	485 checked="false" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	486 label="Trim all sequences from the ends?"
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	487 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	488 <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	489 <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	490 <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	491 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	492 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	493 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	494 <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	495 <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	496 <param name='apply_left_position_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	497 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	498 falsevalue="false" label="Trim
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	499 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	500 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	501 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	502 <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	503 <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	504 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	505 max="3000" value="100" label="Number of
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	506 positions to trim on 5'-end" help="(-trim_left)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	507 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	508 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	509 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	510 <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	511 <param name='apply_right_position_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	512 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	513 falsevalue="false" label="Trim
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	514 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	515 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	516 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	517 <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	518 <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	519 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	520 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	521 of positions to trim on 3'-end"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	522 help="(-trim_right)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	523 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	524 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	525 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	526 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	527 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	528 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	529 <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	530 <param name='apply_percentage_position_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	531 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	532 falsevalue="false" label="Trim sequences
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	533 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	534 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	535 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	536 <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	537 <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	538 <param name='apply_left_percentage_position_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	539 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	540 falsevalue="false" label="Trim sequences
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	541 at the 5'-end by a defined percentage
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	542 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	543 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	544 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	545 <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	546 <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	547 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	548 max="100" value="2" label="Percentage
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	549 of positions to trim on 5'-end" help="(-trim_left_p)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	550 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	551 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	552 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	553 <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	554 <param name='apply_right_percentage_position_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	555 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	556 falsevalue="false" label="Trim
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	557 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	558 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	559 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	560 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	561 <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	562 <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	563 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	564 max="100" value="2" label="Percentage
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	565 of positions to trim on 3'-end" help="(-trim_right_p)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	566 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	567 <when value="false" />
0 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 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	570 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	571 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	572 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	573 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	574 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	575 <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	576 <param name='apply_tail_trimming_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	577 checked="false" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	578 label="Trim tails?" help="By default, no
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	579 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	580 <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	581 <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	582 <param name='apply_a_t_tail_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	583 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	584 falsevalue="false" label="Trim poly-A/T
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	585 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	586 is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	587 <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	588 <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	589 <param name='apply_left_a_t_tail_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	590 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	591 falsevalue="false" label="Trim
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	592 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	593 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	594 is made"/>
6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	595 <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	596 <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	597 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	598 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	599 length of poly-A/T to trim at the 5'-end"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	600 help="(-trim_tail_left)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	601 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	602 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	603 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	604 <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	605 <param name='apply_right_a_t_tail_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	606 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	607 falsevalue="false" label="Trim poly-A/T
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	608 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	609 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	610 <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	611 <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	612 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	613 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	614 length of poly-A/T to trim at the 5'-end"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	615 help="(-trim_tail_right)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	616 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	617 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	618 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	619 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	620 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	621 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	622 <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	623 <param name='apply_ns_tail_trimming_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	624 checked="false" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	625 label="Trim poly-N tail?" help="By
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	626 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	627 <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	628 <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	629 <param name='apply_left_ns_tail_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	630 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	631 falsevalue="false" label="Trim
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	632 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	633 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	634 <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	635 <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	636 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	637 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	638 length of poly-N to trim at the 5'-end"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	639 help="(-trim_ns_left)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	640 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	641 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	642 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	643 <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	644 <param name='apply_right_ns_tail_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	645 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	646 falsevalue="false" label="Trim
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	647 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	648 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	649 <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	650 <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	651 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	652 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	653 length of poly-N to trim at the 5'-end"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	654 help="(-trim_ns_right)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	655 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	656 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	657 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	658 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	659 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	660 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	661 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	662 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	663 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	664 <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	665 <param name='apply_quality_trimming_treatments' type='boolean'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	666 checked="true" truevalue="true" falsevalue="false"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	667 label="Trim sequence by quality score?"
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	668 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	669 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	670 <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	671 <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	672 <param name='apply_left_quality_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	673 type='boolean' checked="false" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	674 falsevalue="false" label="Trim sequence
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	675 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	676 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	677 <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	678 <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	679 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	680 value="20" label="Quality score threshold to
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	681 trim positions" help="(-trim_qual_left)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	682 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	683 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	684 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	685 <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	686 <param name='apply_right_quality_trimming_treatments'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	687 type='boolean' checked="true" truevalue="true"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	688 falsevalue="false" label="Trim sequence
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	689 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	690 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	691 <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	692 <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	693 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	694 value="20" label="Quality score threshold to
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	695 trim positions" help="(-trim_qual_right)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	696 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	697 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	698 </conditional>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	699 <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	700 display="radio" label="Type of quality score calculation
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	701 to use" help="By default, min is used. (-trim_qual_type)">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	702 <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	703 <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	704 <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	705 <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	706 </param>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	707 <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	708 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	709 score to calculated value" help="By default, 'less than'
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	710 is used. (-trim_qual_rule)">
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	711 <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	712 <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	713 <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	714 </param>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	715 <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	716 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	717 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	718 stop at the first base that fails the rule defined, use a
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	719 window size of 1 (default value). (-trim_qual_window)"/>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	720 <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	721 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	722 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	723 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	724 be less or equal to the window size. The default value
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	725 is 1. (-trim_qual_step)"/>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	726 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	727 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	728 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	729 </when>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	730 <when value="false" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	731 </conditional>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	732
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	733 <param name="graph_stats" type="select" multiple="True" label="Which statistics should be calculated included in the graph_data file" help="(-graph_stats)">
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	734 <option value="ld" selected="True">Length distribution</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	735 <option value="gc" selected="True">GC content distribution</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	736 <option value="qd" selected="True">Base quality distribution</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	737 <option value="ns" selected="True">Occurence of N</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	738 <option value="pt" selected="True">Poly-A/T tails</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	739 <option value="ts" selected="True">Tag sequence check</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	740 <option value="aq" selected="True">Assembly quality measure</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	741 <option value="de" selected="True">Sequence duplication - exact only</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	742 <option value="da" selected="True">Sequence duplication - exact + 5'/3'</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	743 <option value="sc" selected="True">Sequence complexity</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	744 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	745 </param>
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	746 </inputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	747
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	748 <outputs>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	749 <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	750 from_work_dir="good_sequences.fastq"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	751 label="Good sequences of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	752 <filter>seq_type['seq_type_opt'] == "single"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	753 </data>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	754 <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	755 from_work_dir="rejected_sequences.fastq"
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	756 label="Rejected sequences of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	757 <filter>seq_type['seq_type_opt'] == "single"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	758 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	759
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	760 <data format="fastq" name="good_sequences_1_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	761 from_work_dir="good_sequences_1.fastq"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	762 label="Good sequences for R1 of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	763 <filter>seq_type['seq_type_opt'] == "paired"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	764 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	765 <data format="fastq" name="good_sequences_1_singletons_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	766 from_work_dir="good_sequences_1_singletons.fastq"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	767 label="Good singleton sequences for R1 of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	768 <filter>seq_type['seq_type_opt'] == "paired"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	769 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	770 <data format="fastq" name="rejected_sequence_1_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	771 from_work_dir="rejected_sequences_1.fastq"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	772 label="Rejected sequences for R1 of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	773 <filter>seq_type['seq_type_opt'] == "paired"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	774 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	775 <data format="fastq" name="good_sequences_2_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	776 from_work_dir="good_sequences_2.fastq"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	777 label="Good sequences for R2 of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	778 <filter>seq_type['seq_type_opt'] == "paired"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	779 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	780 <data format="fastq" name="good_sequences_2_singletons_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	781 from_work_dir="good_sequences_2_singletons.fastq"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	782 label="Good singleton sequences for R2 of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	783 <filter>seq_type['seq_type_opt'] == "paired"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	784 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	785 <data format="fastq" name="rejected_sequence_2_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	786 from_work_dir="rejected_sequences_2.fastq"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	787 label="Rejected sequences for R2 of ${on_string} (PRINSEQ)" >
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	788 <filter>seq_type['seq_type_opt'] == "paired"</filter>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	789 </data>
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	790
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	791 <data format="html" name="html_file"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	792 from_work_dir="stats_html.html"
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	793 label="Summary of ${tool.name} on ${on_string} summary" />
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	794 </outputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	795
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	796 <tests>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	797 <test>
2 6912790a4287 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty bebatut parents: 0 diff changeset	798 <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	799 <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	800 <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	801 <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	802 <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	803 <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	804 <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	805 <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	806 <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	807 <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	808 <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	809 <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	810 <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	811 <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	812 <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	813 <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	814 <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	815 <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	816 <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	817 <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	818 <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	819 <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	820 <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	821 <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	822 <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	823 <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	824 <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	825 <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	826 <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	827 <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	828 <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	829 <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	830
3 10ac5c567b73 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d bebatut parents: 2 diff changeset	831 <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	832 </test>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	833 </tests>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	834
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	835 <help><![CDATA[
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	836
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	837 What it does
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	838
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	839 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	840 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	841 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	842
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	843 -----
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	844
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	845 Input
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	846
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	847 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	848
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	849 @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	850 GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	851 +
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	852 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	853
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	854 -----
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	855
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	856 Parameters
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	857
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	858 The parameters are numerous in PRINSEQ given the wanted treatments.
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	859
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	860 Several filter treatments are proposed:
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	861
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	862 - Filters based on sequence length
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	863 - Filters based on quality score
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	864 - Filters based on base content
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	865
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	866 And several trimming treatments eliminate sequence parts:
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	867 - Trim of ends
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	868 - Trim of tails
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	869 - Trim based quality score
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	870
acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	871 All these treaments can be customed using the proposed parameters.
0 65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	872
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	873 -----
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	874
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	875 Output
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	876
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	877 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	878 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	879
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	880 ]]>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	881 </help>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	882
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	883 <citations>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty bebatut parents: diff changeset	884 <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	885 </citations>
4 acaf871de2ea planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty bebatut parents: 3 diff changeset	886 </tool>

Mercurial > repos > bebatut > prinseq

annotate prinseq.xml @ 4:acaf871de2ea draft default tip