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annotate qfilt.xml @ 0:94e7fce14cfd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit a91f1a9caaff225bea14afd9f7ede25769b02121
author iuc
date Mon, 18 Jun 2018 16:55:03 -0400
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94e7fce14cfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt commit a91f1a9caaff225bea14afd9f7ede25769b02121
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1 <?xml version="1.0"?>
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2 <tool id="qfilt" version="1.0.0" name="qfilt">
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3 <description>filter sequencing data using simple heuristics</description>
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4 <requirements>
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5 <requirement type="package" version="0.0.1">qfilt</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 qfilt -o '$filtered_output'
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9 #if str($options.advanced) == 'advanced':
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10 -q $options.qscore
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11 -l $options.length
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12 $options.split
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13 #if $options.replace and $options.remove:
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14 -P '$options.replace'
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15 -R '$options.remove'
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16 #elif $options.mode:
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17 -m $options.mode
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18 #end if
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19 #if $options.prefix:
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20 -t $options.mismatch
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21 -T '$options.prefix'
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22 #end if
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23 -f $options.output_format
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24 $options.tolerate_homopolymeric $options.tolerate_ambiguous
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25 #end if
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26 #if $input_data.format == 'fastq':
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27 -Q '$input_data.fastq'
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28 #else:
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29 -F '$input_data.fasta'
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30 '$input_data.qual'
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31 #end if
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32 ]]></command>
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33 <inputs>
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34 <conditional name="input_data">
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35 <param name="format" type="select" label="Additional options">
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36 <option value="fastq">FASTQ</option>
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37 <option value="fastaq">FASTA+QUAL</option>
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38 </param>
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39 <when value="fastq">
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40 <param name="fastq" argument="-Q" type="data" format="fastq" label="Input FASTA" help="FASTQ File" />
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41 </when>
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42 <when value="fastaq">
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43 <param name="fasta" argument="-F" type="data" format="fasta" label="Input FASTA" help="FASTA File" />
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44 <param name="qual" argument="-F" type="data" format="qual" label="Input QUAL" help="FASTQ File" />
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45 </when>
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46 </conditional>
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47
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48 <conditional name="options">
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49 <param name="advanced" type="select" label="Additional options">
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50 <option value="defaults">Use defaults</option>
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51 <option value="advanced">Specify additional parameters</option>
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52 </param>
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53 <when value="defaults"/>
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54 <when value="advanced">
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55 <param name="qscore" argument="-q" type="integer" value="20" label="QScore" help="minimum per-base quality score below which a read will be split or truncated" />
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56 <param name="length" argument="-l" type="integer" value="50" label="Length" help="minimum retained fragment LENGTH" />
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57 <param name="mode" argument="-m" type="integer" value="0" label="Mode" help="MODE is a 3-bitmask (an integer in [0-7], default=0)" />
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58 <param name="split" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Split" help="when encountering a low q-score, split instead of truncate" />
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59 <param name="tolerate_homopolymeric" argument="-p" type="boolean" truevalue="-p" falsevalue="" label="Tolerate Homopolymeric" help="tolerate low q-score homopolymeric regions" />
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60 <param name="tolerate_ambiguous" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Tolerate Ambiguous" help="tolerate low q-score ambiguous nucleotides" />
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61 <param name="replace" argument="-P" type="text" label="Replace" help="rather than splitting or truncating, replace low quality bases with CHAR this option OVERRIDES all -m mode options" />
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62 <param name="remove" argument="-R" type="text" label="Remove" help="rather than splitting or truncating, remove reads which contain more than COUNT low quality bases this option only works in COMBINATION with the -P (punch) option" />
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63 <param name="prefix" argument="-T" type="text" label="Prefix" help="if supplied, only reads with this PREFIX are retained, and the PREFIX is stripped from each contributing read" />
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64 <param name="mismatch" argument="-t" type="integer" value="0" label="Mismatch" help="if PREFIX is supplied, prefix matching tolerates at most MISMATCH mismatches" />
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65 <param name="output_format" argument="-f" type="select" label="Format" help="output in FASTA or FASTQ format (default=FASTA)" >
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66 <option value="FASTA">FASTA</option>
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67 <option value="FASTQ">FASTQ</option>
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68 </param>
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69 </when>
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70 </conditional>
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71 </inputs>
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72 <outputs>
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73 <data format="fasta" name="filtered_output">
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74 <change_format>
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75 <when input="output_format" value="FASTQ" format="fastq" />
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76 </change_format>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="fastq" value="qfilt-in1.fastq" />
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82 <output file="qfilt-out1.fa" ftype="fasta" name="filtered_output" />
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83 </test>
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84 <test>
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85 <param name="format" value="fastq" />
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86 <param name="fastq" value="qfilt-in1.fastq" />
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87 <param name="advanced" value="advanced" />
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88 <param name="tolerate_homopolymeric" value="False" />
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89 <output file="qfilt-out2.fa" ftype="fasta" name="filtered_output" />
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90 </test>
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91 <test>
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92 <param name="fasta" value="qfilt-in2.fa" />
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93 <param name="qual" value="qfilt-in2.qual" />
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94 <param name="format" value="fastaq" />
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95 <output file="qfilt-out3.fa" ftype="fasta" name="filtered_output" />
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99 qfilt
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100 =====
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101
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102 This simple program is meant to filter sequencing data with the option to:
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103
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104 - Remove or split reads with poor quality scores
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105 - Retain only fragments from reads that are tagged with a given 5' sequence.
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106
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107 ^^^^^^^^
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108
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109 Example Output
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110
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111 >GM98SRO01B77KU rank=0000671 x=796.0 y=1996.0 length=58
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112
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113 CCACGCGTATCGATGTCGACTTTTTTTTCTTTTCTTACATAGTAG
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114
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115 >GM98SRO01BA3RP rank=0000953 x=419.5 y=1603.5 length=87
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116
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117 CTGATGCTGCACCAACTGTACTCCCTCGCGATA
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118
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119 >GM98SRO01E1BKW rank=0001233 x=1948.0 y=846.0 length=66
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120
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121 TACAGTTGGTGCAGCATCAGAAAAGTACGACATCGATACGCGTGGTCCTCGCGA
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122
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123 >GM98SRO01DVVNY rank=0001304 x=1476.0 y=636.5 length=84
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124
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125 ACGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
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126
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127 >GM98SRO01D6FIX rank=0001416 x=1596.0 y=1415.0 length=91
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128
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129 CGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
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130 ]]></help>
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131 <citations>
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132 <citation type="bibtex">
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133 @UNPUBLISHED{spond,
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134 author = "Sergei Kosakovsky Pond",
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135 title = "HyPhy: Hypothesis Testing using Phylogenies",
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136 year = "2000",
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137 note = "http://hyphy.org/",
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138 url = "http://hyphy.org/"}
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139 </citation>
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140 </citations>
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141 </tool>