annotate prinseq.xml @ 4:654b3a274ed5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
author iuc
date Wed, 07 Jul 2021 09:22:27 +0000
parents 02befcb391f5
children 1ee282794de3
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654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
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1 <tool id="prinseq" name="PRINSEQ" version="@TOOL_VERSION+galaxy1">
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2 <description>to process quality of sequences</description>
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3 <macros>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
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4 <token name="@TOOL_VERSION">0.20.4</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION">prinseq</requirement>
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8 </requirements>
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9
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="" />
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12 <regex match="ERROR"
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13 source="stderr"
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14 level="fatal"
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15 description="" />
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16 <regex match="WARNING"
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17 source="stderr"
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18 level="warning"
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19 description="" />
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20 </stdio>
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22 <version_command>
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23 <![CDATA[
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24 prinseq-lite.pl --version
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25 ]]>
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26 </version_command>
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27
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28 <command>
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29 <![CDATA[
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30 mkdir tmp/
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
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31
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
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32 &&
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34 prinseq-lite.pl
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35 #if $seq_type.seq_type_opt == "single":
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36 -fastq '$seq_type.input_singles'
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37 #if $seq_type.input_singles.is_of_type('fastqillumina'):
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38 -phred64
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39 #end if
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40 #elif $seq_type.seq_type_opt == "paired":
2
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41 -fastq '$seq_type.input_mate1'
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42 -fastq2 '$seq_type.input_mate2'
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43 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
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44 #import sys
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45 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
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46 #end if
1
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47 #if $seq_type.input_mate1.is_of_type('fastqillumina'):
0
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48 -phred64
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49 #end if
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50 #else
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51 -fastq '$seq_type.input_collection.forward'
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52 -fastq2 '$seq_type.input_collection.reverse'
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53 #if $seq_type.input_collection.forward.is_of_type('fastqillumina'):
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54 -phred64
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55 #end if
0
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56 #end if
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57
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58 -out_good "tmp/good_sequences"
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59 -out_bad "tmp/rejected_sequences"
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60
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61 #if $filter_treatments.apply_filter_treatments == "true":
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62 #set length_filter_treatments=$filter_treatments.length_filter_treatments
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63 #if $length_filter_treatments.apply_length_filter_treatments == "true":
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64 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments
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65 #if $min_length_filter_treatments.apply_min_length_filter_treatments == "true":
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66 -min_len $min_length_filter_treatments.min_length_filter_treatment_value
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67 #end if
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68
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69 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments
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70 #if $max_length_filter_treatments.apply_max_length_filter_treatments == "true":
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71 -max_len $max_length_filter_treatments.max_length_filter_treatment_value
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72 #end if
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73 #end if
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74
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75 #set quality_filter_treatments=$filter_treatments.quality_filter_treatments
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76 #if $quality_filter_treatments.apply_quality_filter_treatments == "true":
2
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77 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
0
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78 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true":
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79 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
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80 #end if
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81
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82 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments
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83 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments == "true":
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84 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
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85 #end if
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86
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87 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments
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diff changeset
88 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
89 #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
90 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
91 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
92 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
93
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
94 #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
95 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
96 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
97 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
98 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
99 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
100
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
101 #set base_content_filter_treatments=$filter_treatments.base_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
102 #if $base_content_filter_treatments.apply_base_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
103 #set GC_perc_content_filter_treatments=$base_content_filter_treatments.GC_perc_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
104 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
105 #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
106 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
107 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
108 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
109
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
110 #set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
111 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
112 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
113 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
114 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
115
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
116 #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
117 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
118 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
119 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
120
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
121 #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
122 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
123 -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
124 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
125
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
126 $base_content_filter_treatments.apply_other_base_content_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
127 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
128
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
129 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
130 #if $complexity_filter_treatments.apply_complexity_filter_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
131 -lc_method $complexity_filter_treatments.method_complexity_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
132 -lc_threshold $complexity_filter_treatments.threshold_complexity_filter_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
133 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
134
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
135 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
136
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
137 #if $trimming_treatments.apply_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
138 #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
139 #if $length_trimming_treatments.apply_length_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
140 -trim_to_len $length_trimming_treatments.length_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
141 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
142
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
143 #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
144 #if $position_trimming_treatments.apply_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
145 #set nb_position_trimming_treatments=$position_trimming_treatments.nb_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
146 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
147 #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
148 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
149 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
150 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
151
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
152 #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
153 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
154 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
155 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
156 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
157
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
158 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
159 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
160 #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
161 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
162 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
163 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
164
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
165 #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
166 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
167 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
168 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
169 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
170 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
171
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
172 #set tail_trimming_treatments=$trimming_treatments.tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
173 #if $tail_trimming_treatments.apply_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
174 #set a_t_tail_trimming_treatments=$tail_trimming_treatments.a_t_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
175 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
176 #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
177 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
178 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
179 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
180
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
181 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
182 #if $right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
183 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
184 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
185 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
186
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
187 #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
188 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
189 #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
190 #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
191 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
192 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
193
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
194 #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
195 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
196 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
197 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
198 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
199 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
200
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
201 #set quality_trimming_treatments=$trimming_treatments.quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
202 #if $quality_trimming_treatments.apply_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
203 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
204 #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
205 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
206 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
207
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
208 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
209 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments == "true":
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
210 -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
211 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
212
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
213 -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
214 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
215 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
216 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
217 #end if
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
218
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
219 #end if
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
220
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
221 #*
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
222 -graph_stats "$graph_stats"
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
223 -graph_data tmp/stats.gd
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
224
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
225 &&
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
226
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
227 prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
228 *#
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
229 ]]>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
230 </command>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
231
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
232 <inputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
233 <conditional name="seq_type">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
234 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
235 <option value="single" selected="true">Single-end</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
236 <option value="paired">Paired-end</option>
4
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
237 <option value="paired_collection">Paired Collection</option>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
238 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
239 <when value="single">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
240 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
241 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
242 <when value="paired">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
243 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
244 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
245 </when>
4
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
246 <when value="paired_collection">
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
247 <param name="input_collection" type="data_collection" collection_type="paired" label="FASTQ collection" help="FASTQ data in a paired collection" />
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
248 </when>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
249 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
250
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
251 <conditional name="filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
252 <param name="apply_filter_treatments" type="select" label="Apply filter treatments?">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
253 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
254 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
255 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
256 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
257 <conditional name="length_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
258 <param name="apply_length_filter_treatments" type="select" label="Filter sequence based on their length?" help="By default, sequences smaller than 60 bp are removed. No top threshold is defined">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
259 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
260 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
261 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
262 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
263 <conditional name="min_length_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
264 <param name="apply_min_length_filter_treatments" type="select" label="Filter too small sequences?" help="By default, sequences smaller than 60 bp are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
265 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
266 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
267 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
268 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
269 <param name="min_length_filter_treatment_value" type="integer" min="0" max="3000" value="60" label="Minimum length threshold to conserve sequences" help="(-min_len)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
270 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
271 <when value="false" />
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
272 </conditional>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
273 <conditional name="max_length_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
274 <param name="apply_max_length_filter_treatments" type="select" label="Filter too big sequences?" help="By default, no treatment based on a maximal length is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
275 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
276 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
277 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
278 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
279 <param name="max_length_filter_treatment_value" type="integer" min="0" max="3000" value="1000" label="Maximal length threshold to conserve sequences" help="(-max_len)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
280 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
281 <when value="false" />
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
282 </conditional>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
283 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
284 <when value="false" />
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
285 </conditional>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
286 <conditional name="quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
287 <param name="apply_quality_filter_treatments" type="select" label="Filter sequences based on quality score?" help="By default, sequences with a mean score below 15 are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
288 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
289 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
290 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
291 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
292 <conditional name="min_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
293 <param name="apply_min_quality_filter_treatments" type="select" label="Filter sequences based on their minimum score?" help="By default, no treatment based on a minimum score is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
294 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
295 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
296 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
297 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
298 <param name="min_quality_filter_treatment_value" type="integer" min="0" max="40" value="2" label="Minimum score threshold to conserve sequences" help="(-min_qual_score)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
299 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
300 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
301 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
302 <conditional name="max_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
303 <param name="apply_max_quality_filter_treatments" type="select" label="Filter sequences based on their maximum score?" help="By default, no treatment based on a minimum score is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
304 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
305 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
306 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
307 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
308 <param name="max_quality_filter_treatment_value" type="integer" min="0" max="40" value="38" label="Maximum score threshold to conserve sequences" help="(-max_qual_score)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
309 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
310 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
311 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
312 <conditional name="mean_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
313 <param name="apply_mean_quality_filter_treatments" type="select" label="Filter sequences based on their mean score?" help="By default, sequences with a mean score below 15 are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
314 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
315 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
316 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
317 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
318 <conditional name="min_mean_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
319 <param name="apply_min_mean_quality_filter_treatments" type="select" label="Filter sequences based with too small mean score?" help="By default, sequences with a mean score below 15 are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
320 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
321 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
322 </param>
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
323 <when value="true">
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
324 <param name="min_mean_quality_filter_treatment_value" type="integer" min="0" max="40" value="15" label="Minimum mean score threshold to conserve sequences" help="(-min_qual_mean)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
325 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
326 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
327 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
328 <conditional name="max_mean_quality_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
329 <param name="apply_max_mean_quality_filter_treatments" type="select" label="Filter sequences based with too high mean score?" help="By default, no treatment based on a maximum mean score is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
330 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
331 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
332 </param>
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
333 <when value="true">
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
334 <param name="max_mean_quality_filter_treatment_value" type="integer" min="0" max="40" value="40" label="Maximum mean score threshold to conserve sequences" help="(-max_qual_mean)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
335 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
336 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
337 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
338 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
339 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
340 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
341 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
342 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
343 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
344 <conditional name="base_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
345 <param name="apply_base_content_filter_treatments" type="select" label="Filter sequences based on their base content?" help="By default, sequences with more than 2% of N bases are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
346 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
347 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
348 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
349 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
350 <conditional name="GC_perc_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
351 <param name="apply_GC_perc_content_filter_treatments" type="select" label="Filter sequences based on their GC percentage?" help="By default, no treatment based on GC percentage is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
352 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
353 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
354 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
355 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
356 <conditional name="min_GC_perc_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
357 <param name="apply_min_GC_perc_content_filter_treatments" type="select" label="Filter sequences with too small GC percentage?" help="By default, no treatment based on GC percentage is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
358 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
359 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
360 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
361 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
362 <param name="min_GC_perc_content_filter_treatment_value" type="integer" min="0" max="100" value="10" label="Minimal GC percentage threshold to conserve sequences" help="(-min_gc)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
363 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
364 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
365 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
366 <conditional name="max_GC_perc_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
367 <param name="apply_max_GC_perc_content_filter_treatments" type="select" label="Filter sequences with too high GC percentage?" help="By default, no treatment based on GC percentage is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
368 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
369 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
370 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
371 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
372 <param name="max_GC_perc_content_filter_treatment_value" type="integer" min="0" max="100" value="90" label="Maximal GC percentage threshold to conserve sequences" help="(-max_gc)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
373 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
374 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
375 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
376 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
377 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
378 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
379 <conditional name="N_number_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
380 <param name="apply_N_number_content_filter_treatments" type="select" label="Filter sequences based on their number of N bases?" help="By default, no treatment based on N number is made.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
381 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
382 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
383 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
384 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
385 <param name="N_number_content_filter_treatment_value" type="integer" min="0" max="3000" value="10" label="Maximal N number threshold to conserve sequences" help="(-ns_max_n)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
386 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
387 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
388 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
389 <conditional name="N_percentage_content_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
390 <param name="apply_N_percentage_content_filter_treatments" type="select" label="Filter sequences based on their percentage of N bases?" help="By default, sequences with more than 2% of N bases are removed.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
391 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
392 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
393 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
394 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
395 <param name="N_percentage_content_filter_treatment_value" type="integer" min="0" max="100" value="2" label="Maximal N percentage threshold to conserve sequences" help="(-ns_max_p)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
396 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
397 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
398 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
399 <param name='apply_other_base_content_filter_treatments' type='boolean' truevalue="-noniupac" falsevalue="" checked="false" label="Filter sequences with characters other than A, T, C, G and N?" help="By default, this treatment is not made. (-noniupac)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
400 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
401 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
402 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
403 <conditional name="complexity_filter_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
404 <param name="apply_complexity_filter_treatments" type="select" label="Filter sequences based on their complexity?" help="By default, no complexity filter is applied.">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
405 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
406 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
407 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
408 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
409 <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help="(-lc_method)">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
410 <option value="dust">Dust</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
411 <option value="entropy" >Entropy</option>
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
412 </param>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
413 <param name="threshold_complexity_filter_treatments" type="integer" min="0" max="100" value="2" label="Threshold value used to filter sequences by sequence complexity" help="The dust method uses the threshold as maximum allowed score and the entropy method as minimum allowed value.(-lc_threshold)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
414 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
415 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
416 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
417 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
418 <when value="false" />
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
419 </conditional>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
420
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
421 <conditional name="trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
422 <param name="apply_trimming_treatments" type="select" label="Apply trimming treatments?" help="">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
423 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
424 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
425 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
426 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
427 <conditional name="length_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
428 <param name="apply_length_trimming_treatments" type="select" label="Trim all sequences from the 3'-end to a defined length?" help="By default, no length trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
429 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
430 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
431 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
432 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
433 <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Length of sequences after trimming" help="(-trim_to_len)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
434 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
435 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
436 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
437 <conditional name="position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
438 <param name="apply_position_trimming_treatments" type="select" label="Trim all sequences from the ends?" help="By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
439 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
440 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
441 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
442 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
443 <conditional name="nb_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
444 <param name="apply_nb_position_trimming_treatments" type="select" label="Trim sequences by a defined number of positions?" help="By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
445 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
446 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
447 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
448 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
449 <conditional name="left_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
450 <param name="apply_left_position_trimming_treatments" type="select" label="Trim sequences at the 5'-end by a defined number of positions?" help="By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
451 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
452 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
453 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
454 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
455 <param name="left_position_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 5'-end" help="(-trim_left)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
456 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
457 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
458 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
459 <conditional name="right_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
460 <param name="apply_right_position_trimming_treatments" type="select" label="Trim sequences at the 3'-end by a defined number of positions?" help="By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
461 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
462 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
463 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
464 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
465 <param name="right_position_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 3'-end" help="(-trim_right)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
466 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
467 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
468 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
469 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
470 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
471 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
472 <conditional name="percentage_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
473 <param name="apply_percentage_position_trimming_treatments" type="select" label="Trim sequences by a defined percentage of read length?" help="The trim length is rounded towards the lower integer. By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
474 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
475 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
476 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
477 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
478 <conditional name="left_percentage_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
479 <param name="apply_left_percentage_position_trimming_treatments" type="select" label="Trim sequences at the 5'-end by a defined percentage of read length?" help="The trim length is rounded towards the lower integer. By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
480 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
481 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
482 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
483 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
484 <param name="left_percentage_position_trimming_treatment_value" type="integer" min="0" max="100" value="2" label="Percentage of positions to trim on 5'-end" help="(-trim_left_p)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
485 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
486 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
487 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
488 <conditional name="right_percentage_position_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
489 <param name="apply_right_percentage_position_trimming_treatments" type="select" label="Trim sequences at the 3'-end by a defined percentage of read length?" help="The trim length is rounded towards the lower integer. By default, no position trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
490 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
491 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
492 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
493 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
494 <param name="right_percentage_position_trimming_treatment_value" type="integer" min="0" max="100" value="2" label="Percentage of positions to trim on 3'-end" help="(-trim_right_p)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
495 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
496 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
497 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
498 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
499 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
500 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
501 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
502 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
503 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
504 <conditional name="tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
505 <param name="apply_tail_trimming_treatments" type="select" label="Trim tails?" help="By default, no tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
506 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
507 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
508 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
509 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
510 <conditional name="a_t_tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
511 <param name="apply_a_t_tail_trimming_treatments" type="select" label="Trim poly-A/T tail?" help="By default, no poly-A/T tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
512 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
513 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
514 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
515 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
516 <conditional name="left_a_t_tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
517 <param name="apply_left_a_t_tail_trimming_treatments" type="select" label="Trim poly-A/T tail at the 5'-end?" help="By default, no 5'-end poly-A/T tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
518 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
519 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
520 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
521 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
522 <param name="left_a_t_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" help="(-trim_tail_left)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
523 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
524 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
525 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
526 <conditional name="right_a_t_tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
527 <param name="apply_right_a_t_tail_trimming_treatments" type="select" label="Trim poly-A/T tail at the 3'-end?" help="By default, no 3'-end poly-A/T tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
528 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
529 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
530 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
531 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
532 <param name="right_a_t_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" help="(-trim_tail_right)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
533 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
534 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
535 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
536 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
537 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
538 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
539 <conditional name="ns_tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
540 <param name="apply_ns_tail_trimming_treatments" type="select" label="Trim poly-N tail?" help="By default, no poly-N tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
541 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
542 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
543 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
544 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
545 <conditional name="left_ns_tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
546 <param name="apply_left_ns_tail_trimming_treatments" type="select" label="Trim poly-N tail at the 5'-end?" help="By default, no 5'-end poly-N tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
547 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
548 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
549 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
550 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
551 <param name="left_ns_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" help="(-trim_ns_left)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
552 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
553 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
554 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
555 <conditional name="right_ns_tail_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
556 <param name="apply_right_ns_tail_trimming_treatments" type="select" label="Trim poly-N tail at the 3'-end?" help="By default, no 3'-end poly-N tail trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
557 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
558 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
559 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
560 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
561 <param name="right_ns_tail_trimming_treatment_value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" help="(-trim_ns_right)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
562 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
563 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
564 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
565 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
566 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
567 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
568 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
569 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
570 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
571 <conditional name="quality_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
572 <param name="apply_quality_trimming_treatments" type="select" label="Trim sequence by quality score?" help="By default, a 3'-end trimming is made to remove ends with a minimum quality score over 5 bp below 20">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
573 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
574 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
575 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
576 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
577 <conditional name="left_quality_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
578 <param name="apply_left_quality_trimming_treatments" type="select" label="Trim sequence by quality score from the 5'-end?" help="By default, no 5'-end quality trimming is made">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
579 <option value="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
580 <option value="false" selected="true">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
581 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
582 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
583 <param name="left_quality_trimming_treatment_value" type="integer" min="0" max="40" value="20" label="Quality score threshold to trim positions" help="(-trim_qual_left)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
584 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
585 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
586 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
587 <conditional name="right_quality_trimming_treatments">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
588 <param name="apply_right_quality_trimming_treatments" type="select" label="Trim sequence by quality score from the 3'-end?" help="By default, 3'-end trimming is made based on a score of 20">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
589 <option value="true" selected="true">Yes</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
590 <option value="false">No</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
591 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
592 <when value="true">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
593 <param name="right_quality_trimming_treatment_value" type="integer" min="0" max="40" value="20" label="Quality score threshold to trim positions" help="(-trim_qual_right)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
594 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
595 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
596 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
597 <param name="type_quality_trimming_treatments" type="select" display="radio" label="Type of quality score calculation to use" help="By default, min is used. (-trim_qual_type)">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
598 <option value="min" selected="true">Mininum</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
599 <option value="mean" >Mean</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
600 <option value="max" >Max</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
601 <option value="sum" >Sum</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
602 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
603 <param name="rule_quality_trimming_treatments" type="select" display="radio" label="Rule tu use to compare quality score to calculated value" help="By default, 'less than' is used. (-trim_qual_rule)">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
604 <option value="lt" selected="true">Less than</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
605 <option value="gt" >Greater than</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
606 <option value="et" >Equal to</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
607 </param>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
608 <param name="window_quality_trimming_treatments" type="integer" min="0" max="300" value="1" label="Size of the sliding window used to calculated quality score by type" help="To stop at the first base that fails the rule defined, use a window size of 1 (default value). (-trim_qual_window)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
609 <param name="step_quality_trimming_treatments" type="integer" min="0" max="300" value="1" label="Step size used to move the sliding window" help="To move the window over all quality scores without missing any, the step size sould be less or equal to the window size. The default value is 1. (-trim_qual_step)"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
610 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
611 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
612 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
613 </when>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
614 <when value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
615 </conditional>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
616
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
617 <!--<param name="graph_stats" type="select" multiple="True" label="Which statistics should be calculated included in the graph_data file" help="(-graph_stats)">
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
618 <option value="ld" selected="True">Length distribution</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
619 <option value="gc" selected="True">GC content distribution</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
620 <option value="qd" selected="True">Base quality distribution</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
621 <option value="ns" selected="True">Occurence of N</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
622 <option value="pt" selected="True">Poly-A/T tails</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
623 <option value="ts" selected="True">Tag sequence check</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
624 <option value="aq" selected="True">Assembly quality measure</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
625 <option value="de" selected="True">Sequence duplication - exact only</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
626 <option value="da" selected="True">Sequence duplication - exact + 5'/3'</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
627 <option value="sc" selected="True">Sequence complexity</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
628 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
629 </param>-->
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
630 </inputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
631
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
632 <outputs>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
633 <data format_source="input_singles" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
634 label="${tool.name} on ${on_string}: Good sequences" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
635 <filter>seq_type['seq_type_opt'] == "single"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
636 </data>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
637 <data format_source="input_singles" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
638 label="${tool.name} on ${on_string}: Rejected sequences" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
639 <filter>seq_type['seq_type_opt'] == "single"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
640 </data>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
641
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
642 <data format_source="input_mate1" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
643 label="${tool.name} on ${on_string}: Good sequences for R1" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
644 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
645 </data>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
646 <data format_source="input_mate1" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
647 label="${tool.name} on ${on_string}: Good singleton sequences for R1" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
648 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
649 </data>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
650 <data format_source="input_mate1" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
651 label="${tool.name} on ${on_string}: Rejected sequences for R1" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
652 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
653 </data>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
654 <data format_source="input_mate2" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
655 label="${tool.name} on ${on_string}: Good sequences for R2" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
656 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
657 </data>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
658 <data format_source="input_mate2" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
659 label="${tool.name} on ${on_string}: Good singleton sequences for R2" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
660 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
661 </data>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
662 <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
663 label="${tool.name} on ${on_string}: Rejected sequences for R2" >
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
664 <filter>seq_type['seq_type_opt'] == "paired"</filter>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
665 </data>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
666
4
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
667 <collection name="good_sequences_collection" type="paired">
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
668 <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
669 </collection>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
670
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
671 <collection name="singletons_collection" type="paired">
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
672 <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
673 </collection>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
674
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
675 <collection name="rejected_sequences_collection" type="paired">
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
676 <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
677 </collection>
654b3a274ed5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
iuc
parents: 3
diff changeset
678
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
679 <!--<data format="html" name="html_file" from_work_dir="stats_html.html"
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
680 label="${tool.name} on ${on_string}: Summary" />-->
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
681 </outputs>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
682
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
683 <tests>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
684 <test>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
685 <param name='seq_type_opt' value="single"/>
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
686 <param name="input_singles" value="prinseq_input_sequences.fastq" ftype="fastqsanger"/>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
687 <param name='apply_filter_treatments' value="true"/>
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
688 <param name='apply_length_filter_treatments' value="true"/>
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
689 <param name='apply_min_length_filter_treatments' value="true"/>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
690 <param name="min_length_filter_treatment_value" value="60"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
691 <param name='apply_max_length_filter_treatments' value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
692 <param name='apply_quality_filter_treatments' value="true"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
693 <param name='apply_min_quality_filter_treatments' value="false" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
694 <param name='apply_max_quality_filter_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
695 <param name='apply_mean_quality_filter_treatments' value="true"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
696 <param name='apply_min_mean_quality_filter_treatments' value="true"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
697 <param name="min_mean_quality_filter_treatment_value" value="15"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
698 <param name='apply_max_mean_quality_filter_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
699 <param name='apply_base_content_filter_treatments' value="true"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
700 <param name='apply_GC_perc_content_filter_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
701 <param name='apply_N_number_content_filter_treatments' value="false"/>
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
702 <param name='apply_N_percentage_content_filter_treatments' value="true"/>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
703 <param name="N_percentage_content_filter_treatment_value" value="2"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
704 <param name='apply_other_base_content_filter_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
705 <param name='apply_complexity_filter_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
706 <param name='apply_trimming_treatments' value="true" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
707 <param name='apply_length_trimming_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
708 <param name='apply_position_trimming_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
709 <param name='apply_tail_trimming_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
710 <param name='apply_quality_trimming_treatments' value="true"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
711 <param name='apply_left_quality_trimming_treatments' value="false"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
712 <param name='apply_right_quality_trimming_treatments' value="true" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
713 <param name="right_quality_trimming_treatment_value" value="20"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
714 <param name="type_quality_trimming_treatments" value="min"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
715 <param name="rule_quality_trimming_treatments" value="lt" />
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
716 <param name="window_quality_trimming_treatments" value="1"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
717 <param name="step_quality_trimming_treatments" value="1"/>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
718
3
02befcb391f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
iuc
parents: 2
diff changeset
719 <output name="good_sequence_file" file="prinseq_good_sequences.fastq" ftype="fastqsanger"/>
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
720 </test>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
721 </tests>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
722
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
723 <help><![CDATA[
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
724 **What it does**
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
725
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
726 PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
727 This tool allow to process the sequences with filtering and trimming.
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
728 More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
729
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
730 -----
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
731
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
732 **Input**
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
733
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
734 The input file is sequence file in fastq format (sequences and quality)::
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
735
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
736 @HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
737 GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
738 +
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
739 CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
740
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
741 -----
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
742
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
743 **Parameters**
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
744
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
745 The parameters are numerous in PRINSEQ given the wanted treatments.
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
746
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
747 Several filter treatments are proposed:
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
748
2
74afc47f326c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 1
diff changeset
749 - Filters based on sequence length
0
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
750 - Filters based on quality score
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
751 - Filters based on base content
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
752
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
753 And several trimming treatments eliminate sequence parts:
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
754
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
755 - Trim of ends
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
756 - Trim of tails
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
757 - Trim based quality score
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
758
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
759 All these treaments can be customed using proposed parameters.
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
760
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
761 -----
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
762
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
763 **Output**
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
764
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
765 The output file is a sequence file with sequences and quality from input file
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
766 which have undergone filter and trimming.
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
767 ]]>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
768 </help>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
769
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
770 <citations>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
771 <citation type="doi">10.1093/bioinformatics/btr026</citation>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
772 </citations>
ba78b984a9eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1
iuc
parents:
diff changeset
773 </tool>