Mercurial > repos > bebatut > prinseq

annotate prinseq.xml @ 0:65f03479b3ba draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
author bebatut
date Tue, 27 Oct 2015 12:43:37 -0400
parents
children 6912790a4287
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0
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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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
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2 <description>to process quality of sequences</description>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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3
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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4 <requirements>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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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
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6 </requirements>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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7
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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8 <stdio>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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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
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10 <regex match="ERROR"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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11 source="stderr"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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12 level="fatal"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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13 description="" />
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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14 <regex match="WARNING"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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15 source="stderr"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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16 level="warning"
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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17 description="" />
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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18 </stdio>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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19
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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20 <command><![CDATA[
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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21 perl prinseq-lite.pl
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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22 -fastq $input_sequence_file
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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23 -out_good stdout
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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24 -out_bad null
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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25
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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26 #if $filter_treatments.apply_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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27 #set length_filter_treatments=$filter_treatments.length_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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28 #if $length_filter_treatments.apply_length_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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29 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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30 #if $min_length_filter_treatments.apply_min_length_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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31 -min_len $min_length_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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32 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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33 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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34 #if $max_length_filter_treatments.apply_max_length_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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35 -max_len $min_length_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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36 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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37 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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38
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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39 #set quality_filter_treatments=$filter_treatments.quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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40 #if $quality_filter_treatments.apply_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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41 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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42 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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43 -min_qual_score $min_quality_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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44 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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45 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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46 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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47 -max_qual_score $max_quality_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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48 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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49 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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50 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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51 #set min_mean_quality_filter_treatments=$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
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52 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments:
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53 -min_qual_mean $min_mean_quality_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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54 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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55 #set max_mean_quality_filter_treatments=$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
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56 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments:
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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57 -max_qual_mean $max_mean_quality_filter_treatments.value
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58 #end if
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59 #end if
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60 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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61
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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62 #set base_content_filter_treatments=$filter_treatments.base_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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63 #if $base_content_filter_treatments.apply_base_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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64 #set GC_perc_content_filter_treatments=$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
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65 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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66 #set min_GC_perc_content_filter_treatments=$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
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67 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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68 -min_gc $min_GC_perc_content_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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69 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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70 set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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71 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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72 -max_gc $max_GC_perc_content_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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73 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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74 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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75 #set N_number_content_filter_treatments=$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
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76 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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77 -ns_max_n $N_number_content_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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78 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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79 #set N_percentage_content_filter_treatments=$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
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80 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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81 -ns_max_p $N_percentage_content_filter_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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82 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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83 #if $base_content_filter_treatments.apply_other_base_content_filter_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
84 -noniupac
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
85 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
86 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
87
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
88 #set complexity_filter_treatments=$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
89 #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
90 -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
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parents:
diff changeset
91 -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
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parents:
diff changeset
92 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
93
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
94 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
95
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
96 #if $trimming_treatments.apply_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
97 #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
98 #if $length_trimming_treatments.apply_length_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
99 -trim_to_len $length_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
100 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
101
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
102 #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
103 #if $position_trimming_treatments.apply_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
104 #set nb_position_trimming_treatments=$position_trimming_treatments.nb_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
105 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
106 #set left_position_trimming_treatments=$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
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parents:
diff changeset
107 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
108 -trim_left $left_position_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
109 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
110 #set right_position_trimming_treatments=$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
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parents:
diff changeset
111 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
112 -trim_right $right_position_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
113 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
114 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
115 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
116 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
117 #set left_percentage_position_trimming_treatments=$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
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parents:
diff changeset
118 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
119 -trim_left_p $left_percentage_position_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
120 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
121 #set right_percentage_position_trimming_treatments=$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
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parents:
diff changeset
122 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
123 -trim_right_p $right_percentage_position_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
124 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
125 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
126 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
127
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
128 #set tail_trimming_treatments=$trimming_treatments.tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
129 #if $tail_trimming_treatments.apply_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
130 #set a_t_tail_trimming_treatments=$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
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parents:
diff changeset
131 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
132 #set left_a_t_tail_trimming_treatments=$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
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parents:
diff changeset
133 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
134 -trim_tail_left $left_a_t_tail_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
135 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
136 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
137 #if right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
138 -trim_tail_right $right_a_t_tail_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
139 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
140 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
141 #set ns_tail_trimming_treatments=$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
142 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
143 #set left_ns_tail_trimming_treatments=$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
144 #if $left_ns_tail_trimming_treatments.apply_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
145 -trim_ns_left $left_ns_tail_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
146 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
147 #set right_ns_tail_trimming_treatments=$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
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parents:
diff changeset
148 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
149 -trim_ns_right $right_ns_tail_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
150 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
151 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
152 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
153
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
154 #set quality_trimming_treatments=$trimming_treatments.quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
155 #if $quality_trimming_treatments.apply_quality_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
156 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
157 #if $left_quality_trimming_treatments.apply_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
158 -trim_qual_left $left_quality_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
159 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
160 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
161 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments :
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
162 -trim_qual_right $right_quality_trimming_treatments.value
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
163 #end if
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
164 -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
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parents:
diff changeset
165 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments
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166 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments
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167 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
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168 #end if
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169
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170 #end if
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171
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172 >> $good_sequence_file
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173 ]]>
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174 </command>
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175
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176 <inputs>
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177 <param name="input_sequence_file" type="data" format="fastq" label="Input sequence file" help="The file must be in fastq format for quality scores"/>
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178
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179 <conditional name="filter_treatments">
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180 <param name='apply_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Apply filter treatments?" help=""/>
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181 <when value="yes">
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182 <conditional name="length_filter_treatments">
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183 <param name='apply_length_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequence based on their length?" help="By default, sequences smaller than 60 bp are removed. No top threshold is defined"/>
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184 <when value="yes">
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185 <conditional name="min_length_filter_treatments">
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186 <param name='apply_min_length_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter too small sequences?" help="By default, sequences smaller than 60 bp are removed."/>
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187 <when value="yes">
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188 <param name="value" type="integer" min="0" max="3000" value="60" label="Minimum length threshold to conserve sequences" help=""/>
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189 </when>
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190 </conditional>
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191 <conditional name="max_length_filter_treatments">
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192 <param name='apply_max_length_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter too big sequences?" help="By default, no treatment based on a maximal length is made"/>
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193 <when value="yes">
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194 <param name="value" type="integer" min="0" max="3000" value="1000" label="Maximal length threshold to conserve sequences" help=""/>
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195 </when>
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196 </conditional>
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197 </when>
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198 </conditional>
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199 <conditional name="quality_filter_treatments">
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200 <param name='apply_quality_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on quality score?" help="By default, sequences with a mean score below 15 are removed."/>
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201 <when value="yes">
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202 <conditional name="min_quality_filter_treatments">
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203 <param name='apply_min_quality_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their minimum score?" help="By default, no treatment based on a minimum score is made"/>
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204 <when value="yes">
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205 <param name="value" type="integer" min="0" max="40" value="2" label="Minimum score threshold to conserve sequences" help=""/>
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206 </when>
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207 </conditional>
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208 <conditional name="max_quality_filter_treatments">
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209 <param name='apply_max_quality_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their maximum score?" help="By default, no treatment based on a maximum score is made"/>
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210 <when value="yes">
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211 <param name="value" type="integer" min="0" max="40" value="38" label="Maximum score threshold to conserve sequences" help=""/>
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212 </when>
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213 </conditional>
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214 <conditional name="mean_quality_filter_treatments">
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215 <param name='apply_mean_quality_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on their mean score?" help="By default, sequences with a mean score below 15 are removed."/>
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216 <when value="yes">
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217 <conditional name="min_mean_quality_filter_treatments">
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218 <param name='apply_min_mean_quality_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences with too small mean score?" help="By default, sequences with a mean score below 15 are removed."/>
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219 <when value="yes">
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220 <param name="value" type="integer" min="0" max="40" value="15" label="Minimum mean score threshold to conserve sequences" help=""/>
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221 </when>
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222 </conditional>
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223 <conditional name="max_mean_quality_filter_treatments">
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224 <param name='apply_max_mean_quality_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with too high mean score?" help="By default, no treatment based on a maximum mean score is made"/>
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225 <when value="yes">
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226 <param name="value" type="integer" min="0" max="40" value="40" label="Maximum mean score threshold to conserve sequences" help=""/>
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227 </when>
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228 </conditional>
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229 </when>
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230 </conditional>
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231 </when>
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232 </conditional>
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233 <conditional name="base_content_filter_treatments">
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234 <param name='apply_base_content_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on their base content?" help="By default, sequences with more than 2% of N bases are removed."/>
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235 <when value="yes">
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236 <conditional name="GC_perc_content_filter_treatments">
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237 <param name='apply_GC_perc_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their GC percentage?" help="By default, no treatment based on GC percentage is made."/>
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238 <when value="yes">
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239 <conditional name="min_GC_perc_content_filter_treatments">
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240 <param name='apply_min_GC_perc_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with too small GC percentage?" help="By default, no treatment based on GC percentage is made."/>
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241 <when value="yes">
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242 <param name="value" type="integer" min="0" max="100" value="10" label="Minimal GC percentage threshold to conserve sequences" help=""/>
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243 </when>
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244 </conditional>
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245 <conditional name="max_GC_perc_content_filter_treatments">
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246 <param name='apply_max_GC_perc_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with too high GC percentage?" help="By default, no treatment based on GC percentage is made."/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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247 <when value="yes">
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248 <param name="value" type="integer" min="0" max="100" value="90" label="Maximal GC percentage threshold to conserve sequences" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
249 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
250 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
251 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
252 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
253 <conditional name="N_number_content_filter_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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254 <param name='apply_N_number_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their number of N bases?" help="By default, no treatment based on N number is made."/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
255 <when value="yes">
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256 <param name="value" type="integer" min="0" max="3000" value="10" label="Maximal N number threshold to conserve sequences" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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257 </when>
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258 </conditional>
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259 <conditional name="N_percentage_content_filter_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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260 <param name='apply_N_percentage_content_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on their percentage of N bases?" help="By default, sequences with more than 2% of N bases are removed."/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
261 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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262 <param name="value" type="integer" min="0" max="100" value="2" label="Maximal N percentage threshold to conserve sequences" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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263 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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264 </conditional>
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265 <param name='apply_other_base_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with characters other than A, T, C, G and N?" help="By default, this treatment is not made."/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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266 </when>
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267 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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268 <conditional name="complexity_filter_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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269 <param name='apply_complexity_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their complexity?" help="By default, no complexity filter is applied"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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270 <when value="yes">
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271 <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help="">
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272 <option value="dust">Dust</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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273 <option value="entropy" >Entropy</option>
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274 </param>
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275 <param name="threshold_complexity_filter_treatments" type="integer" min="0" max="100" value="2" label="Threshold value used to filter sequences by sequence complexity" help="The dust method uses the threshold as maximum allowed score and the entropy method as minimum allowed value."/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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276 </when>
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277 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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278 </when>
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279 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
280
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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281 <conditional name="trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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282 <param name='apply_trimming_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Apply trimming treatments?" help=""/>
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diff changeset
283 <when value="yes">
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284 <conditional name="length_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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285 <param name='apply_length_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim all sequences from the 3'-end to a length?" help="By default, no length trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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diff changeset
286 <when value="yes">
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287 <param name="value" type="integer" min="0" max="3000" value="100" label="Length of sequences after trimming" help=""/>
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288 </when>
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289 </conditional>
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290 <conditional name="position_trimming_treatments">
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291 <param name='apply_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim all sequences from the ends?" help="By default, no position trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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292 <when value="yes">
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293 <conditional name="nb_position_trimming_treatments">
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294 <param name='apply_nb_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences by a defined number of positions?" help="By default, no position trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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295 <when value="yes">
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296 <conditional name="left_position_trimming_treatments">
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297 <param name='apply_left_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 5'-end by a defined number of positions?" help="By default, no position trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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298 <when value="yes">
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299 <param name="value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 5'-end" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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300 </when>
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301 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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302 <conditional name="right_position_trimming_treatments">
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303 <param name='apply_right_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 3'-end by a defined number of positions?" help="By default, no position trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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304 <when value="yes">
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305 <param name="value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 3'-end" help=""/>
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306 </when>
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307 </conditional>
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308 </when>
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309 </conditional>
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310 <conditional name="percentage_position_trimming_treatments">
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311 <param name='apply_percentage_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences by a defined percentage of read length?" help="By default, no position trimming is made. The trim length is rounded towards the lower integer"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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312 <when value="yes">
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313 <conditional name="left_percentage_position_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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314 <param name='apply_left_percentage_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 5'-end by a defined percentage of read length?" help="By default, no position trimming is made. The trim length is rounded towards the lower integer"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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315 <when value="yes">
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316 <param name="value" type="integer" min="0" max="100" value="2" label="Percentage of positions to trim on 5'-end" help=""/>
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317 </when>
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318 </conditional>
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319 <conditional name="right_percentage_position_trimming_treatments">
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320 <param name='apply_right_percentage_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 3'-end by a defined percentage of read length?" help="By default, no position trimming is made. The trim length is rounded towards the lower integer"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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321 <when value="yes">
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322 <param name="value" type="integer" min="0" max="100" value="2" label="Percentage of positions to trim on 3'-end" help=""/>
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323 </when>
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324 </conditional>
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325 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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326 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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327 </when>
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328 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
329 <conditional name="tail_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
330 <param name='apply_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim tails?" help="By default, no tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
331 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
332 <conditional name="a_t_tail_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
333 <param name='apply_a_t_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-A/T tail?" help="By default, no poly-A/T tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
334 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
335 <conditional name="left_a_t_tail_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
336 <param name='apply_left_a_t_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-A/T tail at the 5'-end?" help="By default, no 5'-end poly-A/T tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
337 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
338 <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
339 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
340 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
341 <conditional name="right_a_t_tail_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
342 <param name='apply_right_a_t_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-A/T tail at the 5'-end?" help="By default, no 3'-end poly-A/T tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
343 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
344 <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
345 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
346 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
347 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
348 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
349 <conditional name="ns_tail_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
350 <param name='apply_ns_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-N tail?" help="By default, no poly-N tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
351 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
352 <conditional name="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
353 <param name='apply_left_ns_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-N tail at the 5'-end?" help="By default, no 5'-end poly-N tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
354 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
355 <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
356 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
357 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
358 <conditional name="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
359 <param name='apply_right_ns_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-N tail at the 5'-end?" help="By default, no 3'-end poly-N tail trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
360 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
361 <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
362 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
363 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
364 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
365 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
366 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
367 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
368 <conditional name="quality_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
369 <param name='apply_quality_trimming_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Trim sequence by quality score?" help="By default, a 3'-end trimming is made to remove ends with a minimum quality score over 5 bp below 20"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
370 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
371 <conditional name="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
372 <param name='apply_left_quality_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequence by quality score from the 5'-end?" help="By default, no 5'-end quality trimming is made"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
373 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
374 <param name="value" type="integer" min="0" max="40" value="20" label="Quality score threshold to trim positions" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
375 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
376 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
377 <conditional name="right_quality_trimming_treatments">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
378 <param name='apply_right_quality_trimming_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Trim sequence by quality score from the 3'-end?" help="By default, 3'-end trimming is made based on a score of 20"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
379 <when value="yes">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
380 <param name="value" type="integer" min="0" max="40" value="20" label="Quality score threshold to trim positions" help=""/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
381 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
382 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
383 <param name="type_quality_trimming_treatments" type="select" display="radio" label="Type of quality score calculation to use" help="By default, min is used">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
384 <option value="min" selected="true">Mininum</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
385 <option value="mean" >Mean</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
386 <option value="max" >Max</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
387 <option value="sum" >Sum</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
388 </param>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
389 <param name="rule_quality_trimming_treatments" type="select" display="radio" label="Rule tu use to compare quality score to calculated value" help="By default, 'less than' is used">
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
390 <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
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parents:
diff changeset
391 <option value="gt" >Greater than</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
392 <option value="et" >Equal to</option>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
393 </param>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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394 <param name="window_quality_trimming_treatments" type="integer" min="0" max="300" value="1" label="Size of the sliding window used to calculated quality score by type" help="To stop at the first base that fails the rule defined, use a window size of 1 (default value)"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
395 <param name="step_quality_trimming_treatments" type="integer" min="0" max="300" value="1" label="Step size used to move the sliding window" help="To move the window over all quality scores without missing any, the step size sould be less or equal to the window size. The default value is 1."/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
396 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
397 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
398 </when>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
399 </conditional>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
400 </inputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
401
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
402 <outputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
403 <data format="fastq" name="good_sequence_file" metadata_source="input_sequence_file"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
404 </outputs>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
bebatut
parents:
diff changeset
405
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
406 <tests>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
407 <test>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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parents:
diff changeset
408 <param name="input_sequence_file" value="input_sequences.fastq"/>
65f03479b3ba planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 60b4516b1882c91adf8041a586c0a17738f38dbc-dirty
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409 <output name="good_sequence_file" file="output_sequences.fastq"/>
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410 </test>
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411 </tests>
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412
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413 <help><![CDATA[
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414
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415 **What it does**
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416
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417 PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.
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418 This tool allow to process the sequences with filtering and trimming.
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419 More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.
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420
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421 -----
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422
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423 **Input**
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424
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425 The input file is sequence file in fastq format (sequences and quality)::
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426
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427 @HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG
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428 GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT
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429 +
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430 CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF
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431
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432 -----
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433
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434 **Parameters**
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435
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436 The parameters are numerous in PRINSEQ
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437
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438 - Filtering parameters to eliminate sequences
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439 - Filters based on sequence length
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440 - Filters based on quality score
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441 - Filters based on base content
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442 - Trimming parameters to eliminate sequence parts
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443 - Trim of ends
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444 - Trim of tails
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445 - Trim based quality score
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446
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447 -----
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448
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449 **Output**
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450
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451 The output file is a sequence file with sequences and quality from input file
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452 which have undergone filter and trimming.
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453
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454 ]]>
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455 </help>
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456
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457 <citations>
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458 <citation type="doi">10.1093/bioinformatics/btr026</citation>
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459 </citations>
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460 </tool>