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annotate art_solid.xml @ 2:7a12314c5b64 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 97a064489364118d108b0dd2cfb4d9bc53080837-dirty
author iuc
date Thu, 19 Nov 2015 12:32:17 -0500
parents a12ce5668966
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_solid" name="ART SOLiD" version="2014.11.03.0">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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2 <description>simulates SOLiD data</description>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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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_SOLiD
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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 $sam
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12
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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13 #if $rndSeed and $rndSeed > -1:
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14 -r $rndSeed
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15 #end if
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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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17 #if $generate.amplicon.use_amplicon == "amplicon_true":
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18 -A
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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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20 #if $generate.choice == "single_end":
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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21 s
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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22 #else if $generate.choice == "paired_end":
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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23 p
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24 #else:
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25 m
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26 #end if
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27
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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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":
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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34 $generate.LEN_READ
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35 $fold_coverage
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36 #else if $generate.choice == "paired_end":
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37 $generate.LEN_READ_F3
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38 $generate.LEN_READ_F5
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39 $fold_coverage
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40 $generate.fragment_size
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41 $generate.fragment_sd
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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42 #else:
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43 $generate.LEN_READ
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44 $fold_coverage
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45 $generate.fragment_size
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46 $generate.fragment_sd
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47 #end if
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48
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49 #if $generate.amplicon.use_amplicon == "amplicon_true":
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50 #if $generate.choice == "single_end":
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51 $generate.amplicon.reads_per_amplicon
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52 #else:
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53 $generate.amplicon.read_pairs_per_amplicon
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54 #end if
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55 #end if
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56 ]]></command>
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57 <inputs>
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58 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
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59 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
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60
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61 <conditional name="generate">
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62 <param name="choice" type="select" label="Type of data to generate">
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63 <option value="single_end">Single-End</option>
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64 <option value="paired_end">Paired-End</option>
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65 <option value="paired_end">Mate Pair</option>
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66 </param>
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67 <when value="single_end">
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68 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
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69 <expand macro="amplicon" />
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70 </when>
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71 <when value="paired_end">
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72 <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" />
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73 <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" />
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74 <expand macro="frag_len_sd" />
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75 <expand macro="amplicon_pair" />
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76 </when>
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77 <when value="mate_pair">
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78 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
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79 <expand macro="frag_len_sd" />
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80 <expand macro="amplicon_pair" />
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81 </when>
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82 </conditional>
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83
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84 <expand macro="sam" />
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85 <expand macro="rndSeed" />
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86
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87 </inputs>
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88 <outputs>
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89
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90 <!-- Single End -->
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91 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name">
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92 <filter>generate['choice'] == "single_end"</filter>
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93 </data>
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94
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95 <!-- Paired End -->
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96 <data format="fastq" name="output_fq1_paired" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)">
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97 <filter>generate['choice'] == "paired_end"</filter>
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98 </data>
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99 <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)">
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100 <filter>generate['choice'] == "paired_end"</filter>
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101 </data>
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102
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103 <!-- Mate Pair -->
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104 <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)">
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105 <filter>generate['choice'] == "mate_pair"</filter>
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106 </data>
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107 <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)">
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108 <filter>generate['choice'] == "mate_pair"</filter>
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109 </data>
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110
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111 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name">
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112 <filter>sam</filter>
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113 </data>
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114 <!-- todo? map file -->
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115 </outputs>
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116 <tests>
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117 <!-- Single End tests -->
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118 <test>
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119 <param name="rndSeed" value="42" />
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120 <param name="input_seq_file" value="input.fa" />
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121 <param name="LEN_READ" value="25" />
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122 <param name="fold_coverage" value="10" />
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123 <param name="choice" value="single_end" />
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124 <param name="sam" value="False" />
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125
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126 <output name="output_fq1_single" file="art.solid.01.fq" />
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127 </test>
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128 <test>
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129 <param name="rndSeed" value="42" />
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130 <param name="input_seq_file" value="input.fa" />
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131 <param name="fold_coverage" value="20" />
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132 <param name="choice" value="paired_end" />
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133 <param name="LEN_READ_F3" value="50" />
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134 <param name="LEN_READ_F5" value="50" />
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135 <param name="fragment_size" value="75" />
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136 <param name="fragment_sd" value="10" />
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137 <param name="sam" value="True" />
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138
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139 <output name="output_fq1_paired" file="art.solid.02_F3.fq" />
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140 <output name="output_fq2_paired" file="art.solid.02_F5.fq" />
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141 <output name="output_sam" file="art.solid.02.sam" lines_diff="2"/>
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142 </test>
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143 </tests>
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144 <help><![CDATA[
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145 Art SOLiD Simulator
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146 ===================
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147
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148 ART_SOLiD is a simulation program to generate sequence read data of SOLiD
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149 sequencing reads. ART generates reads according to a SOLiD read error profile.
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150 The built-in error profile is an empiricial error profile summarized from large
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151 SOLiD sequencing data. ART has been using for testing or benchmarking a variety
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152 of method or tools for next-generation sequencing data analysis, including read
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153 alignment, de novo assembly, detection of SNP, CNV, or other structure
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154 variation.
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155
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156 art_SOLiD can generate both single-end, matepair, and paired-end of SOLiD
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157 sequencing platform. art_SOLiD also support amplicon sequencing simulation with
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158 RNA references.
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159 ]]></help>
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160 <expand macro="citation" />
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161 </tool>
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162