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comparison art_454.xml @ 0:b98d6fffd00b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
author iuc
date Thu, 11 Jun 2015 11:51:06 -0400
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-1:000000000000 0:b98d6fffd00b
1 <tool id="art_454" name="ART 454" version="2014.11.03.0">
2 <description>simulates pyrosequencing data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="stdio" />
7 <command><![CDATA[
8 art_454 $t
9
10 $aln
11 $sam
12
13 #if $rndSeed and $rndSeed > -1:
14 -r $rndSeed
15 #end if
16
17 #if $c
18 -c $c
19 #end if
20
21 #if $generate.amplicon.use_amplicon == "amplicon_true":
22 #if $generate.choice == "single_end":
23 -A
24 #else:
25 -B
26 #end if
27 #end if
28
29 $input_seq_file
30 output
31
32 #if $generate.choice == "single_end":
33 $fold_coverage
34 #else:
35 $fold_coverage
36 $generate.fragment_size
37 $generate.fragment_sd
38 #end if
39
40 #if $generate.amplicon.use_amplicon == "amplicon_true":
41 #if $generate.choice == "single_end":
42 $generate.amplicon.reads_per_amplicon
43 #else:
44 $generate.amplicon.read_pairs_per_amplicon
45 #end if
46 #end if
47 ;
48 ]]></command>
49 <inputs>
50 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
51 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
52
53 <conditional name="generate">
54 <param name="choice" type="select" label="Type of data to generate">
55 <option value="single_end">Single-End</option>
56 <option value="paired_end">Paired-End</option>
57 </param>
58 <when value="single_end">
59 <expand macro="amplicon" />
60 </when>
61 <when value="paired_end">
62 <expand macro="frag_len_sd" />
63 <expand macro="amplicon_pair" />
64 </when>
65 </conditional>
66
67
68 <expand macro="sam" />
69 <expand macro="aln" />
70
71 <param type="boolean" label="indicate to simulate reads from the built-in GS FLX Titanium profile (-t)" name="t" truevalue="-t" falsevalue="" optional="true" />
72 <param label="specify the number of flow cycles by the sequencer [100 for GS-FLX, 200 for GS-FLX Titanium] (-c)" name="c" type="integer" value="100" optional="true" />
73
74 <expand macro="rndSeed" />
75 </inputs>
76 <outputs>
77 <!-- Single End -->
78 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of 454 sequencing of $input_seq_file.name">
79 <filter>generate['choice'] == "single_end"</filter>
80 </data>
81
82 <!-- Paired End -->
83 <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Forward)">
84 <filter>generate['choice'] != "single_end"</filter>
85 </data>
86 <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Reverse)">
87 <filter>generate['choice'] != "single_end"</filter>
88 </data>
89 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated 454 data to $input_seq_file.name">
90 <filter>sam</filter>
91 </data>
92
93 <!-- Single End -->
94 <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated 454 data to $input_seq_file.name">
95 <filter>aln and generate['choice'] == "single_end"</filter>
96 </data>
97 <!-- Paired End -->
98 <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated 454 data to $input_seq_file.name">
99 <filter>aln and generate['choice'] != "single_end"</filter>
100 </data>
101 <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated 454 data to $input_seq_file.name">
102 <filter>generate['choice'] != "single_end" and generate['amplicon']['use_amplicon'] == "amplicon_true"</filter>
103 </data>
104 </outputs>
105 <tests>
106 <!-- Single End tests -->
107 <test>
108 <param name="rndSeed" value="42" />
109 <param name="input_seq_file" value="input.fa" />
110 <param name="fold_coverage" value="20" />
111 <param name="choice" value="single_end" />
112 <output name="output_fq1_single" file="art.454.01.fq" />
113 </test>
114 <test>
115 <param name="rndSeed" value="42" />
116 <param name="input_seq_file" value="input.fa" />
117 <param name="fold_coverage" value="20" />
118 <param name="choice" value="single_end" />
119 <param name="sam" value="True" />
120 <output name="output_fq1_single" file="art.454.01.fq" />
121 <output name="output_sam" file="art.454.01.sam" lines_diff="2"/>
122 </test>
123 <!-- Paired End tests -->
124 <test>
125 <param name="rndSeed" value="42" />
126 <param name="input_seq_file" value="input.fa" />
127 <param name="fold_coverage" value="20" />
128 <param name="choice" value="paired_end" />
129 <param name="fragment_size" value="105" />
130 <param name="fragment_sd" value="5" />
131 <param name="sam" value="True" />
132 <output name="output_fq1_paired" file="art.454.021.fq" />
133 <output name="output_fq2_paired" file="art.454.022.fq" />
134 <output name="output_sam" file="art.454.02.sam" lines_diff="2"/>
135 </test>
136 </tests>
137 <help><![CDATA[
138 Art 454 Pyrosequencing Simulator
139 ================================
140
141 ART_454 is a simulation program to generate sequence read data of Roche 454
142 Pyrosequencing sequencers. ART generates reads according to the empirical read
143 quality profile and the calibrated error profile of uncall/overcall
144 homopolymers from real 454 read data. ART has been using for testing or
145 benchmarking a variety of method or tools for next-generation sequencing data
146 analysis, including read alignment, de novo assembly, detection of SNP, CNV, or
147 other structure variation.
148
149 art_454 can generate both single-end and paired-end of 454 sequencing platform.
150 Besides for regular genome DNA and cDNA sequencing simulation, art_454 also
151 supports amplicon sequencing. The reference sequences can be either DNA or RNA.
152 ]]></help>
153 <expand macro="citation" />
154 </tool>
155