|
0
|
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
|
