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annotate art_454.xml @ 1:a12ce5668966 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
author iuc
date Thu, 11 Jun 2015 13:50:36 -0400
parents b98d6fffd00b
children bb7e0ccc0029
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b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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1 <tool id="art_454" name="ART 454" version="2014.11.03.0">
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2 <description>simulates pyrosequencing data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1
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6 <expand macro="requirements"/>
0
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7 <expand macro="stdio" />
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8 <command><![CDATA[
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9 art_454 $t
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10
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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11 $aln
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12 $sam
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13
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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14 #if $rndSeed and $rndSeed > -1:
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15 -r $rndSeed
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16 #end if
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17
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18 #if $c
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19 -c $c
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20 #end if
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21
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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22 #if $generate.amplicon.use_amplicon == "amplicon_true":
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23 #if $generate.choice == "single_end":
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24 -A
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25 #else:
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26 -B
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27 #end if
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28 #end if
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29
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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30 $input_seq_file
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31 output
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32
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33 #if $generate.choice == "single_end":
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34 $fold_coverage
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35 #else:
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36 $fold_coverage
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37 $generate.fragment_size
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38 $generate.fragment_sd
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39 #end if
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40
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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41 #if $generate.amplicon.use_amplicon == "amplicon_true":
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42 #if $generate.choice == "single_end":
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43 $generate.amplicon.reads_per_amplicon
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44 #else:
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45 $generate.amplicon.read_pairs_per_amplicon
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46 #end if
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47 #end if
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48 ;
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49 ]]></command>
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50 <inputs>
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51 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
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52 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
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53
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54 <conditional name="generate">
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55 <param name="choice" type="select" label="Type of data to generate">
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56 <option value="single_end">Single-End</option>
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57 <option value="paired_end">Paired-End</option>
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58 </param>
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59 <when value="single_end">
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60 <expand macro="amplicon" />
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61 </when>
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62 <when value="paired_end">
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63 <expand macro="frag_len_sd" />
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64 <expand macro="amplicon_pair" />
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65 </when>
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66 </conditional>
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67
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68
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69 <expand macro="sam" />
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70 <expand macro="aln" />
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71
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72 <param type="boolean" label="indicate to simulate reads from the built-in GS FLX Titanium profile (-t)" name="t" truevalue="-t" falsevalue="" optional="true" />
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73 <param label="specify the number of flow cycles by the sequencer [100 for GS-FLX, 200 for GS-FLX Titanium] (-c)" name="c" type="integer" value="100" optional="true" />
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74
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75 <expand macro="rndSeed" />
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76 </inputs>
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77 <outputs>
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78 <!-- Single End -->
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79 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of 454 sequencing of $input_seq_file.name">
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80 <filter>generate['choice'] == "single_end"</filter>
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81 </data>
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82
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83 <!-- Paired End -->
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84 <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Forward)">
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85 <filter>generate['choice'] != "single_end"</filter>
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86 </data>
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87 <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Reverse)">
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88 <filter>generate['choice'] != "single_end"</filter>
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89 </data>
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90 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated 454 data to $input_seq_file.name">
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91 <filter>sam</filter>
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92 </data>
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93
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94 <!-- Single End -->
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95 <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated 454 data to $input_seq_file.name">
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96 <filter>aln and generate['choice'] == "single_end"</filter>
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97 </data>
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98 <!-- Paired End -->
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99 <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated 454 data to $input_seq_file.name">
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100 <filter>aln and generate['choice'] != "single_end"</filter>
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101 </data>
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102 <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated 454 data to $input_seq_file.name">
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103 <filter>generate['choice'] != "single_end" and generate['amplicon']['use_amplicon'] == "amplicon_true"</filter>
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104 </data>
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105 </outputs>
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106 <tests>
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107 <!-- Single End tests -->
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108 <test>
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109 <param name="rndSeed" value="42" />
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110 <param name="input_seq_file" value="input.fa" />
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111 <param name="fold_coverage" value="20" />
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112 <param name="choice" value="single_end" />
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113 <output name="output_fq1_single" file="art.454.01.fq" />
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114 </test>
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115 <test>
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116 <param name="rndSeed" value="42" />
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117 <param name="input_seq_file" value="input.fa" />
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118 <param name="fold_coverage" value="20" />
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119 <param name="choice" value="single_end" />
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120 <param name="sam" value="True" />
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121 <output name="output_fq1_single" file="art.454.01.fq" />
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122 <output name="output_sam" file="art.454.01.sam" lines_diff="2"/>
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123 </test>
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124 <!-- Paired End tests -->
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125 <test>
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126 <param name="rndSeed" value="42" />
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127 <param name="input_seq_file" value="input.fa" />
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128 <param name="fold_coverage" value="20" />
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129 <param name="choice" value="paired_end" />
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130 <param name="fragment_size" value="105" />
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131 <param name="fragment_sd" value="5" />
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132 <param name="sam" value="True" />
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133 <output name="output_fq1_paired" file="art.454.021.fq" />
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134 <output name="output_fq2_paired" file="art.454.022.fq" />
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135 <output name="output_sam" file="art.454.02.sam" lines_diff="2"/>
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136 </test>
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137 </tests>
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138 <help><![CDATA[
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139 Art 454 Pyrosequencing Simulator
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140 ================================
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141
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142 ART_454 is a simulation program to generate sequence read data of Roche 454
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143 Pyrosequencing sequencers. ART generates reads according to the empirical read
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144 quality profile and the calibrated error profile of uncall/overcall
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145 homopolymers from real 454 read data. ART has been using for testing or
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146 benchmarking a variety of method or tools for next-generation sequencing data
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147 analysis, including read alignment, de novo assembly, detection of SNP, CNV, or
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148 other structure variation.
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149
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150 art_454 can generate both single-end and paired-end of 454 sequencing platform.
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151 Besides for regular genome DNA and cDNA sequencing simulation, art_454 also
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152 supports amplicon sequencing. The reference sequences can be either DNA or RNA.
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153 ]]></help>
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154 <expand macro="citation" />
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155 </tool>
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156