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annotate trinityrnaseq_norm.xml @ 4:d5580071d910

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Update commandline to detect successful completion
author Jim Johnson <jj@umn.edu>
date Mon, 11 Nov 2013 11:08:56 -0600
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1 <tool id="trinityrnaseq_norm" name="Trinity read normalization" version="0.0.2">
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2 <!-- Written by Jeremy Goecks, modified by Josh Bowden for normalization proceedure, now maintained here by bhaas -->
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3 <description>Pre-process RNA-seq data to reduce coverage of highly covered areas</description>
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4 <requirements>
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5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
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6 </requirements>
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7 <command>
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8 ## symlink input in work_dir
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9 #if str($inputs.paired_or_single) == "paired":
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10 ln -s $inputs.left_input left_reads &amp;&amp;
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11 ln -s $inputs.right_input right_reads &amp;&amp;
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12 #else:
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13 ln -s $inputs.input single_reads &amp;&amp;
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14 #end if
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15 \${TRINITY_HOME}/util/normalize_by_kmer_coverage.pl --JM $JM --max_cov $max_cov
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16 ## Inputs.
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17 #if str($inputs.paired_or_single) == "paired":
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18 --left left_reads --right right_reads
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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 $inputs.pe_reads_unordered
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25 #if str($inputs.library_type) != "None":
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26 --SS_lib_type $inputs.library_type
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27 #end if
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28 $inputs.pairs_together
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29 $inputs.parallel_stats
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30 #else:
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31 --single single_reads
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32 #if str($inputs.input.ext) == 'fa':
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33 --seqType fa
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34 #else:
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35 --seqType fq
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36 #end if
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37 #if str($inputs.library_type) != "None":
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38 --SS_lib_type $inputs.library_type
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39 #end if
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40 #end if
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41 #if $kmer_size:
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42 --KMER_SIZE $kmer_size
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43 #end if
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44 #if $max_pct_stdev:
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45 --max_pct_stdev $max_pct_stdev
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46 #end if
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47 ## direct stdio to output
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48 | tee $trinity_coverage_normalization_log &amp;&amp;
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49 #if str($inputs.paired_or_single) == "paired":
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50 cp left_reads.normalized* $output_left &amp;&amp;
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51 cp right_reads.normalized* $output_right
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52 #else:
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53 cp single_reads.normalized* $output_single
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54 #end if
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55 </command>
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56 <inputs>
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57 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
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58 <option value="1G">1G</option>
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59 <option value="10G">10G</option>
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60 <option value="20G">20G</option>
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61 <option value="50G">50G</option>
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62 <option value="100G">100G</option>
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63 </param>
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64
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65 <param name="max_cov" type="select" label="max_cov" help="Read coverage in terms of maximum covarge to keep">
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66 <option value="30">30</option>
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67 <option value="40">40</option>
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68 <option value="50">50</option>
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69 <option value="60">60</option>
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70 <option value="70">70</option>
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71 <option value="100">100</option>
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72 </param>
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73
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74 <conditional name="inputs">
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75 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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76 <option value="paired">Paired</option>
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77 <option value="single">Single</option>
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78 </param>
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79 <when value="paired">
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80 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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81 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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82 <param name="library_type" type="select" label="Strand-specific Library Type">
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83 <option value="None">None</option>
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84 <option value="FR">FR</option>
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85 <option value="RF">RF</option>
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86 </param>
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87 <param name="pe_reads_unordered" type="boolean" truevalue="--PE_reads_unordered" falsevalue="" checked="false" label="set if the input paired-end reads are not identically ordered"/>
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88 <param name="pairs_together" type="boolean" truevalue="--pairs_together" falsevalue="" checked="false" label="process paired reads by averaging stats between pairs and retaining linking info"/>
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89 <param name="parallel_stats" type="boolean" truevalue="--PARALLEL_STATS" falsevalue="" checked="false" label="generate read stats in parallel for paired reads" help="(Figure 2X Inchworm memory requirement)"/>
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90 </when>
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91 <when value="single">
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92 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
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93 <param name="library_type" type="select" label="Strand-specific Library Type">
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94 <option value="None">None</option>
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95 <option value="F">F</option>
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96 <option value="R">R</option>
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97 </param>
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98 </when>
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99 </conditional>
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100 <param name="kmer_size" type="integer" value="" optional="true" label="KMER SIZE" help="default: 25">
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101 <validator type="in_range" message="kmer size between 3 and 200" min="3" max="200"/>
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102 </param>
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103 <param name="max_pct_stdev" type="integer" value="" optional="true" label="maximum pct of mean for stdev of kmer coverage across read" help="default: 100">
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104 <validator type="in_range" message="kmer size between 10 and 100" min="10" max="100"/>
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105 </param>
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106
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107 </inputs>
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108 <stdio>
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109 <exit_code range="1:" level="fatal" description="Failed" />
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110 <regex match="Error"
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111 source="stdout"
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112 level="fatal"
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113 description="Failed" />
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114 </stdio>
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115 <outputs>
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116 <!-- I have not found a way to do condional outputs so all potential output files are specified and some will be empty -->
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117 <data format="txt" name="trinity_coverage_normalization_log" label="${tool.name} on ${on_string}: log" />
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118 <data format_source="left_input" name="output_left" label="${tool.name} on ${on_string}: Normalized left reads">
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119 <filter>inputs['paired_or_single'] == "paired"</filter>
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120 </data>
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121 <data format_source="right_input" name="output_right" label="${tool.name} on ${on_string}: Normalized right reads">
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122 <filter>inputs['paired_or_single'] == "paired"</filter>
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123 </data>
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124 <data format_source="input" name="output_single" label="${tool.name} on ${on_string}: Normalized reads">
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125 <filter>inputs['paired_or_single'] == "single"</filter>
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126 </data>
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127 </outputs>
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128 <tests>
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129 <test>
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130 <param name="JM" value="1G"/>
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131 <param name="max_cov" value="30"/>
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132 <param name="paired_or_single" value="single"/>
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133 <param name="input" ftype="fastq" value="reads.left.fq"/>
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134 <param name="library_type" value="None"/>
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135 <output name="trinity_coverage_normalization_log">
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136 <assert_contents>
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137 <has_text text="Normalization complete." />
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138 </assert_contents>
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139 </output>
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140 <output name="output_single">
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141 <assert_contents>
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142 <has_text text="ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT" />
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143 </assert_contents>
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144 </output>
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145 </test>
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146 <test>
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147 <param name="JM" value="1G"/>
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148 <param name="max_cov" value="30"/>
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149 <param name="paired_or_single" value="paired"/>
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150 <param name="left_input" ftype="fastq" value="reads.left.fq"/>
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151 <param name="right_input" ftype="fastq" value="reads.right.fq"/>
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152 <param name="library_type" value="None"/>
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153 <param name="pe_reads_unordered" value="False"/>
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154 <param name="pairs_together" value="False"/>
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155 <param name="parallel_stats" value="False"/>
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156 <output name="trinity_coverage_normalization_log">
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157 <assert_contents>
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158 <has_text text="Normalization complete." />
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159 </assert_contents>
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160 </output>
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161 <output name="output_left">
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162 <assert_contents>
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163 <has_text text="CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG" />
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164 </assert_contents>
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165 </output>
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166 <output name="output_right">
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167 <assert_contents>
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168 <has_text text="CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC" />
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169 </assert_contents>
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170 </output>
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171 </test>
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172 </tests>
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173 <help>
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174 Runs script Trinity_ script util/normalize_by_kmer_coverage.pl which reduces data sizes with minimal impact on recovered transcripts when used by Trinity.pl.
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175
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176 .. _Trinity: http://trinityrnaseq.sourceforge.net
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177 </help>
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178 </tool>