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1 <?xml version="1.0"?>
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2 <tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="0.0.1">
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3
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4 <description>Read Normalization</description>
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5 <requirements>
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6 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
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7 <requirement type="set_environment">TRINITY_HOME</requirement>
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8
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9 </requirements>
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10 <command interperter="perl"> \$TRINITY_HOME/util/insilico_read_normalization.pl
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11 --JM $JM
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12 --max_cov $maximum_coverage
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13
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14 ## Inputs.
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15 #if str($inputs.paired_or_single) == "paired":
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16
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17 --left $inputs.left_input --right $inputs.right_input
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18
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19 #if $inputs.left_input.ext == 'fa':
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20 --seqType fa
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21 #else:
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22 --seqType fq
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23 #end if
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24
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25 ## Additional parameters.
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26 #if str($inputs.additional_params.use_additional) == "yes":
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27
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28 #if str($inputs.additional_params.library_type) != "None":
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29 --SS_lib_type $inputs.additional_params.library_type
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30 #end if
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31
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32 $inputs.additional_params.pairs_together
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33 --CPU $inputs.additional_params.CPU
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34 $inputs.additional_params.PARALLEL_STATS
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35 --KMER_SIZE $inputs.additional_params.KMER_SIZE
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36 --max_pct_stdev $inputs.additional_params.max_pct_stdev
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37
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38 #end if
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39
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40
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41 #else:
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42
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43 --single $inputs.input
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44
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45 #if str($inputs.input.ext) == 'fa':
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46 --seqType fa
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47 #else:
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48 --seqType fq
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49 #end if
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50
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51 ## Additional parameters.
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52 #if str($inputs.additional_params.use_additional) == "yes":
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53
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54 #if str($inputs.additional_params.library_type) != "None":
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55 --SS_lib_type $inputs.additional_params.library_type
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56 #end if
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57
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58 ##$inputs.additional_params.pairs_together
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59 --CPU $inputs.additional_params.CPU
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60 ##$inputs.additional_params.PARALLEL_STATS
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61 --KMER_SIZE $inputs.additional_params.KMER_SIZE
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62 --max_pct_stdev $inputs.additional_params.max_pct_stdev
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63
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64 #end if
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65
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66 #end if
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67
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68
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69
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70 ## direct to output
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71 > $insilico_read_normalization_log 2>&1
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72
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73 </command>
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74
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75 <inputs>
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76 <param name="JM" type="select" label="JM" help="--JM < string > ; Amount of memory to allocate to Jellyfish for Kmer catalog construction">
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77 <option value="1G">1G</option>
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78 <option value="10G">10G</option>
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79 <option value="20G">20G</option>
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80 <option value="50G">50G</option>
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81 </param>
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82
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83 <param name="maximum_coverage" type="integer" value="25" label="Maximum Coverage" help="--max_cov < int > ; targeted maximum coverage for reads"/>
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84
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85 <conditional name="inputs">
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86 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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87 <option value="paired">Paired</option>
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88 <option value="single">Single</option>
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89 </param>
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90
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91 <when value="paired">
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92 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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93 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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94
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95 <conditional name="additional_params">
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96 <param name="use_additional" type="select" label="Use Additional Params?">
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97 <option value="no">No</option>
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98 <option value="yes">Yes</option>
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99 </param>
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100 <when value="no"/>
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101 <when value="yes">
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102 <param name="library_type" type="select" label="Strand-specific Library Type">
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103 <option value="None">None</option>
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104 <option value="FR">FR</option>
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105 <option value="RF">RF</option>
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106 </param>
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107 <param name="pairs_together" type="boolean" label="--pairs_together" help="process paired reads by averaging stats between pairs and retaining linking info" truevalue="--pairs_together" falsevalue="" checked="true" />
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108 <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU < int > ; Number of CPUs to use (Maximum limit is 30 core)" />
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109 <param name="PARALLEL_STATS" type="boolean" label="--PARALLEL_STATS" help="Generate read stats in parallel for paired reads" truevalue="--PARALLEL_STATS" falsevalue="" checked="true" />
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110 <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" />
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111 <param name="max_pct_stdev" type="integer" value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/>
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112 </when>
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113 </conditional>
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114 </when>
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115
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116 <when value="single">
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117 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
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118
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119 <conditional name="additional_params">
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120 <param name="use_additional" type="select" label="Use Additional Params?">
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121 <option value="no">No</option>
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122 <option value="yes">Yes</option>
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123 </param>
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124 <when value="no"/>
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125 <when value="yes">
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126 <param name="library_type" type="select" label="Strand-specific Library Type">
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127 <option value="None">None</option>
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128 <option value="F">F</option>
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129 <option value="R">R</option>
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130 </param>
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131 <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU < int > ; Number of CPUs to use (Maximum limit is 30 core)" />
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132 <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" />
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133 <param name="max_pct_stdev" type="integer" value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/>
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134 </when>
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135 </conditional>
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136 </when>
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137 </conditional>
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138
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139
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140 </inputs>
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141
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142 <outputs>
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143 <data format="txt" name="insilico_read_normalization_log" label="${tool.name} on ${on_string}: log" />
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144 <data format="fastq" name="left_normalized_read" label="${tool.name} on ${on_string}: Left Read" from_work_dir="left.norm.fq"/>
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145 <data format="fastq" name="right_normalized_read" label="${tool.name} on ${on_string}: Right Read" from_work_dir="right.norm.fq"/>
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146 </outputs>
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147
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148
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149 <tests/>
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150 <help>Insilico Read Normalization</help>
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151
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152 </tool>
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