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Add trinityrnaseq_norm and transcriptsToOrfs tools
author Jim Johnson <jj@umn.edu>
date Thu, 05 Sep 2013 08:08:21 -0500
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1:a34ce2b18877 2:5eb99d21ef0d
1 <tool id="trinityrnaseq_norm" name="Trinity read normalization" version="0.0.2">
2 <!-- Written by Jeremy Goecks, modified by Josh Bowden for normalization proceedure, now maintained here by bhaas -->
3 <description>Pre-process RNA-seq data to reduce coverage of highly covered areas</description>
4 <requirements>
5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
6 </requirements>
7 <command>
8 ## symlink input in work_dir
9 #if str($inputs.paired_or_single) == "paired":
10 ln -s $inputs.left_input left_reads &amp;&amp;
11 ln -s $inputs.right_input right_reads &amp;&amp;
12 #else:
13 ln -s $inputs.input single_reads &amp;&amp;
14 #end if
15 \${TRINITY_HOME}/util/normalize_by_kmer_coverage.pl --JM $JM --max_cov $max_cov
16 ## Inputs.
17 #if str($inputs.paired_or_single) == "paired":
18 --left left_reads --right right_reads
19 #if $inputs.left_input.ext == 'fa':
20 --seqType fa
21 #else:
22 --seqType fq
23 #end if
24 $inputs.pe_reads_unordered
25 #if str($inputs.library_type) != "None":
26 --SS_lib_type $inputs.library_type
27 #end if
28 $inputs.pairs_together
29 $inputs.parallel_stats
30 #else:
31 --single single_reads
32 #if str($inputs.input.ext) == 'fa':
33 --seqType fa
34 #else:
35 --seqType fq
36 #end if
37 #if str($inputs.library_type) != "None":
38 --SS_lib_type $inputs.library_type
39 #end if
40 #end if
41 #if $kmer_size:
42 --KMER_SIZE $kmer_size
43 #end if
44 #if $max_pct_stdev:
45 --max_pct_stdev $max_pct_stdev
46 #end if
47 ## direct stdio to output
48 | tee $trinity_coverage_normalization_log &amp;&amp;
49 #if str($inputs.paired_or_single) == "paired":
50 cp left_reads.normalized* $output_left &amp;&amp;
51 cp right_reads.normalized* $output_right
52 #else:
53 cp single_reads.normalized* $output_single
54 #end if
55 </command>
56 <inputs>
57 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
58 <option value="1G">1G</option>
59 <option value="10G">10G</option>
60 <option value="20G">20G</option>
61 <option value="50G">50G</option>
62 <option value="100G">100G</option>
63 </param>
64
65 <param name="max_cov" type="select" label="max_cov" help="Read coverage in terms of maximum covarge to keep">
66 <option value="30">30</option>
67 <option value="40">40</option>
68 <option value="50">50</option>
69 <option value="60">60</option>
70 <option value="70">70</option>
71 <option value="100">100</option>
72 </param>
73
74 <conditional name="inputs">
75 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
76 <option value="paired">Paired</option>
77 <option value="single">Single</option>
78 </param>
79 <when value="paired">
80 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
81 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
82 <param name="library_type" type="select" label="Strand-specific Library Type">
83 <option value="None">None</option>
84 <option value="FR">FR</option>
85 <option value="RF">RF</option>
86 </param>
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"/>
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"/>
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)"/>
90 </when>
91 <when value="single">
92 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
93 <param name="library_type" type="select" label="Strand-specific Library Type">
94 <option value="None">None</option>
95 <option value="F">F</option>
96 <option value="R">R</option>
97 </param>
98 </when>
99 </conditional>
100 <param name="kmer_size" type="integer" value="" optional="true" label="KMER SIZE" help="default: 25">
101 <validator type="in_range" message="kmer size between 3 and 200" min="3" max="200"/>
102 </param>
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">
104 <validator type="in_range" message="kmer size between 10 and 100" min="10" max="100"/>
105 </param>
106
107 </inputs>
108 <stdio>
109 <exit_code range="1:" level="fatal" description="Failed" />
110 <regex match="Error"
111 source="stdout"
112 level="fatal"
113 description="Failed" />
114 </stdio>
115 <outputs>
116 <!-- I have not found a way to do condional outputs so all potential output files are specified and some will be empty -->
117 <data format="txt" name="trinity_coverage_normalization_log" label="${tool.name} on ${on_string}: log" />
118 <data format_source="left_input" name="output_left" label="${tool.name} on ${on_string}: Normalized left reads">
119 <filter>inputs['paired_or_single'] == "paired"</filter>
120 </data>
121 <data format_source="right_input" name="output_right" label="${tool.name} on ${on_string}: Normalized right reads">
122 <filter>inputs['paired_or_single'] == "paired"</filter>
123 </data>
124 <data format_source="input" name="output_single" label="${tool.name} on ${on_string}: Normalized reads">
125 <filter>inputs['paired_or_single'] == "single"</filter>
126 </data>
127 </outputs>
128 <tests>
129 <test>
130 <param name="JM" value="1G"/>
131 <param name="max_cov" value="30"/>
132 <param name="paired_or_single" value="single"/>
133 <param name="input" ftype="fastq" value="reads.left.fq"/>
134 <param name="library_type" value="None"/>
135 <output name="trinity_coverage_normalization_log">
136 <assert_contents>
137 <has_text text="Normalization complete." />
138 </assert_contents>
139 </output>
140 <output name="output_single">
141 <assert_contents>
142 <has_text text="ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT" />
143 </assert_contents>
144 </output>
145 </test>
146 <test>
147 <param name="JM" value="1G"/>
148 <param name="max_cov" value="30"/>
149 <param name="paired_or_single" value="paired"/>
150 <param name="left_input" ftype="fastq" value="reads.left.fq"/>
151 <param name="right_input" ftype="fastq" value="reads.right.fq"/>
152 <param name="library_type" value="None"/>
153 <param name="pe_reads_unordered" value="False"/>
154 <param name="pairs_together" value="False"/>
155 <param name="parallel_stats" value="False"/>
156 <output name="trinity_coverage_normalization_log">
157 <assert_contents>
158 <has_text text="Normalization complete." />
159 </assert_contents>
160 </output>
161 <output name="output_left">
162 <assert_contents>
163 <has_text text="CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG" />
164 </assert_contents>
165 </output>
166 <output name="output_right">
167 <assert_contents>
168 <has_text text="CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC" />
169 </assert_contents>
170 </output>
171 </test>
172 </tests>
173 <help>
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.
175
176 .. _Trinity: http://trinityrnaseq.sourceforge.net
177 </help>
178 </tool>