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comparison art_solid.xml @ 0:03a48ad6b460 draft

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author iuc
date Fri, 10 Apr 2015 22:46:25 -0400
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1 <tool id="art_solid" name="ART SOLiD" version="2014.11.03.0">
2 <description>simulates SOLiD data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="stdio" />
7 <command><![CDATA[
8 art_SOLiD
9
10 $sam
11
12 #if $rndSeed and $rndSeed > -1:
13 -r $rndSeed
14 #end if
15
16 #if $generate.amplicon.use_amplicon == "amplicon_true":
17 -A
18
19 #if $generate.choice == "single_end":
20 s
21 #else if $generate.choice == "paired_end":
22 p
23 #else:
24 m
25 #end if
26
27 #end if
28
29 $input_seq_file
30 output
31
32 #if $generate.choice == "single_end":
33 $generate.LEN_READ
34 $fold_coverage
35 #else if $generate.choice == "paired_end":
36 $generate.LEN_READ_F3
37 $generate.LEN_READ_F5
38 $fold_coverage
39 $generate.fragment_size
40 $generate.fragment_sd
41 #else:
42 $generate.LEN_READ
43 $fold_coverage
44 $generate.fragment_size
45 $generate.fragment_sd
46 #end if
47
48 #if $generate.amplicon.use_amplicon == "amplicon_true":
49 #if $generate.choice == "single_end":
50 $generate.amplicon.reads_per_amplicon
51 #else:
52 $generate.amplicon.read_pairs_per_amplicon
53 #end if
54 #end if
55 ]]></command>
56 <inputs>
57 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
58 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
59
60 <conditional name="generate">
61 <param name="choice" type="select" label="Type of data to generate">
62 <option value="single_end">Single-End</option>
63 <option value="paired_end">Paired-End</option>
64 <option value="paired_end">Mate Pair</option>
65 </param>
66 <when value="single_end">
67 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
68 <expand macro="amplicon" />
69 </when>
70 <when value="paired_end">
71 <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" />
72 <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" />
73 <expand macro="frag_len_sd" />
74 <expand macro="amplicon_pair" />
75 </when>
76 <when value="mate_pair">
77 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
78 <expand macro="frag_len_sd" />
79 <expand macro="amplicon_pair" />
80 </when>
81 </conditional>
82
83 <expand macro="sam" />
84 <expand macro="rndSeed" />
85
86 </inputs>
87 <outputs>
88
89 <!-- Single End -->
90 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name">
91 <filter>generate['choice'] == "single_end"</filter>
92 </data>
93
94 <!-- Paired End -->
95 <data format="fastq" name="output_fq1_paired" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)">
96 <filter>generate['choice'] == "paired_end"</filter>
97 </data>
98 <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)">
99 <filter>generate['choice'] == "paired_end"</filter>
100 </data>
101
102 <!-- Mate Pair -->
103 <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)">
104 <filter>generate['choice'] == "mate_pair"</filter>
105 </data>
106 <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)">
107 <filter>generate['choice'] == "mate_pair"</filter>
108 </data>
109
110 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name">
111 <filter>sam</filter>
112 </data>
113 <!-- todo? map file -->
114 </outputs>
115 <tests>
116 <!-- Single End tests -->
117 <test>
118 <param name="rndSeed" value="42" />
119 <param name="input_seq_file" value="input.fa" />
120 <param name="LEN_READ" value="25" />
121 <param name="fold_coverage" value="10" />
122 <param name="choice" value="single_end" />
123 <param name="sam" value="False" />
124
125 <output name="output_fq1_single" file="art.solid.01.fq" />
126 </test>
127 <test>
128 <param name="rndSeed" value="42" />
129 <param name="input_seq_file" value="input.fa" />
130 <param name="fold_coverage" value="20" />
131 <param name="choice" value="paired_end" />
132 <param name="LEN_READ_F3" value="50" />
133 <param name="LEN_READ_F5" value="50" />
134 <param name="fragment_size" value="75" />
135 <param name="fragment_sd" value="10" />
136 <param name="sam" value="True" />
137
138 <output name="output_fq1_paired" file="art.solid.02_F3.fq" />
139 <output name="output_fq2_paired" file="art.solid.02_F5.fq" />
140 <output name="output_sam" file="art.solid.02.sam" lines_diff="2"/>
141 </test>
142 </tests>
143 <help><![CDATA[
144 Art SOLiD Simulator
145 ===================
146
147 ART_SOLiD is a simulation program to generate sequence read data of SOLiD
148 sequencing reads. ART generates reads according to a SOLiD read error profile.
149 The built-in error profile is an empiricial error profile summarized from large
150 SOLiD sequencing data. ART has been using for testing or benchmarking a variety
151 of method or tools for next-generation sequencing data analysis, including read
152 alignment, de novo assembly, detection of SNP, CNV, or other structure
153 variation.
154
155 art_SOLiD can generate both single-end, matepair, and paired-end of SOLiD
156 sequencing platform. art_SOLiD also support amplicon sequencing simulation with
157 RNA references.
158 ]]></help>
159 <expand macro="citation" />
160 </tool>
161