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+ − 1 <?xml version="1.0"?>
+ − 2 <tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="r20140717">
+ − 3
+ − 4 <!-- Written by Anmol J. Hemrom -->
+ − 5 <description>Read Normalization</description>
+ − 6
+ − 7 <requirements>
+ − 8 <requirement type="package" version="r20140717">trinityrnaseq</requirement>
+ − 9 </requirements>
+ − 10
+ − 11
+ − 12 <command interperter="perl"> \$TRINITY_HOME/util/insilico_read_normalization.pl
+ − 13 --JM $JM
+ − 14 --max_cov $maximum_coverage
+ − 15
+ − 16 ## Inputs.
+ − 17 #if str($inputs.paired_or_single) == "paired":
+ − 18
+ − 19 --left $inputs.left_input --right $inputs.right_input
+ − 20
+ − 21 #if $inputs.left_input.ext == 'fa':
+ − 22 --seqType fa
+ − 23 #else:
+ − 24 --seqType fq
+ − 25 #end if
+ − 26
+ − 27 ## Additional parameters.
+ − 28 #if str($inputs.additional_params.use_additional) == "yes":
+ − 29
+ − 30 #if str($inputs.additional_params.library_type) != "None":
+ − 31 --SS_lib_type $inputs.additional_params.library_type
+ − 32 #end if
+ − 33
+ − 34 $inputs.additional_params.pairs_together
+ − 35 --CPU $inputs.additional_params.CPU
+ − 36 $inputs.additional_params.PARALLEL_STATS
+ − 37 --KMER_SIZE $inputs.additional_params.KMER_SIZE
+ − 38 --max_pct_stdev $inputs.additional_params.max_pct_stdev
+ − 39
+ − 40 #end if
+ − 41
+ − 42
+ − 43 #else:
+ − 44
+ − 45 --single $inputs.input
+ − 46
+ − 47 #if str($inputs.input.ext) == 'fa':
+ − 48 --seqType fa
+ − 49 #else:
+ − 50 --seqType fq
+ − 51 #end if
+ − 52
+ − 53 ## Additional parameters.
+ − 54 #if str($inputs.additional_params.use_additional) == "yes":
+ − 55
+ − 56 #if str($inputs.additional_params.library_type) != "None":
+ − 57 --SS_lib_type $inputs.additional_params.library_type
+ − 58 #end if
+ − 59
+ − 60 ##$inputs.additional_params.pairs_together
+ − 61 --CPU $inputs.additional_params.CPU
+ − 62 ##$inputs.additional_params.PARALLEL_STATS
+ − 63 --KMER_SIZE $inputs.additional_params.KMER_SIZE
+ − 64 --max_pct_stdev $inputs.additional_params.max_pct_stdev
+ − 65
+ − 66 #end if
+ − 67
+ − 68 #end if
+ − 69
+ − 70
+ − 71
+ − 72 ## direct to output
+ − 73 > $insilico_read_normalization_log 2>&1
+ − 74
+ − 75 </command>
+ − 76
+ − 77
+ − 78 <inputs>
+ − 79 <param name="JM" type="select" label="JM" help="--JM < string > ; Amount of memory to allocate to Jellyfish for Kmer catalog construction">
+ − 80 <option value="1G">1G</option>
+ − 81 <option value="10G">10G</option>
+ − 82 <option value="20G">20G</option>
+ − 83 <option value="50G">50G</option>
+ − 84 </param>
+ − 85
+ − 86 <param name="maximum_coverage" type="integer" value="25" label="Maximum Coverage" help="--max_cov < int > ; targeted maximum coverage for reads"/>
+ − 87
+ − 88 <conditional name="inputs">
+ − 89 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+ − 90 <option value="paired">Paired</option>
+ − 91 <option value="single">Single</option>
+ − 92 </param>
+ − 93
+ − 94 <when value="paired">
+ − 95 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+ − 96 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+ − 97
+ − 98 <conditional name="additional_params">
+ − 99 <param name="use_additional" type="select" label="Use Additional Params?">
+ − 100 <option value="no">No</option>
+ − 101 <option value="yes">Yes</option>
+ − 102 </param>
+ − 103 <when value="no"/>
+ − 104 <when value="yes">
+ − 105 <param name="library_type" type="select" label="Strand-specific Library Type">
+ − 106 <option value="None">None</option>
+ − 107 <option value="FR">FR</option>
+ − 108 <option value="RF">RF</option>
+ − 109 </param>
+ − 110 <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" />
+ − 111 <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)" />
+ − 112 <param name="PARALLEL_STATS" type="boolean" label="--PARALLEL_STATS" help="Generate read stats in parallel for paired reads" truevalue="--PARALLEL_STATS" falsevalue="" checked="true" />
+ − 113 <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" />
+ − 114 <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"/>
+ − 115 </when>
+ − 116 </conditional>
+ − 117 </when>
+ − 118
+ − 119
+ − 120 <when value="single">
+ − 121 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+ − 122
+ − 123 <conditional name="additional_params">
+ − 124 <param name="use_additional" type="select" label="Use Additional Params?">
+ − 125 <option value="no">No</option>
+ − 126 <option value="yes">Yes</option>
+ − 127 </param>
+ − 128 <when value="no"/>
+ − 129 <when value="yes">
+ − 130 <param name="library_type" type="select" label="Strand-specific Library Type">
+ − 131 <option value="None">None</option>
+ − 132 <option value="F">F</option>
+ − 133 <option value="R">R</option>
+ − 134 </param>
+ − 135 <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)" />
+ − 136 <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" />
+ − 137 <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"/>
+ − 138 </when>
+ − 139 </conditional>
+ − 140 </when>
+ − 141 </conditional>
+ − 142
+ − 143
+ − 144 </inputs>
+ − 145
+ − 146 <outputs>
+ − 147 <data format="txt" name="insilico_read_normalization_log" label="${tool.name} on ${on_string}: log" />
+ − 148 <data format="fastq" name="left_normalized_read" label="${tool.name} on ${on_string}: Left Read" from_work_dir="left.norm.fq"/>
+ − 149 <data format="fastq" name="right_normalized_read" label="${tool.name} on ${on_string}: Right Read" from_work_dir="right.norm.fq"/>
+ − 150 </outputs>
+ − 151
+ − 152
+ − 153 <tests/>
+ − 154 <help>Insilico Read Normalization</help>
+ − 155
+ − 156 </tool>
+ − 157
