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comparison insilico_read_normalization.xml @ 0:60d9e2097e02 draft

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author anmoljh
date Thu, 27 Aug 2015 09:16:16 -0400
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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 &gt; $insilico_read_normalization_log 2&gt;&amp;1
74
75 </command>
76
77
78 <inputs>
79 <param name="JM" type="select" label="JM" help="--JM &lt; string &gt; ; 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 &lt; int &gt; ; 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 &lt; int &gt; ; 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 &lt; int &gt; ; 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