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comparison art_illumina.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_illumina" name="ART Illumina" version="2014.11.03.0">
2 <description>simulates sequencing data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="stdio" />
7 <command><![CDATA[
8 art_illumina
9
10 #if str($sam) == "-s":
11 --samout
12 #end if
13
14 #if not str($aln) == "-a":
15 --noALN
16 #end if
17
18 #if str($generate.choice) == "paired_end":
19 --paired
20 --mflen $generate.fragment_size
21 --sdev $generate.fragment_sd
22 #else if str($generate.choice) == "mate_pair":
23 --matepair
24 --mflen $generate.fragment_size
25 --sdev $generate.fragment_sd
26 #end if
27
28 --in $input_seq_file
29 --len $read_length
30 --fcov $fold_coverage
31
32 $amplicon
33
34 --insRate $insRate
35 --insRate2 $insRate2
36 --delRate $delRate
37 --delRate2 $delRate2
38
39 #if $rndSeed and $rndSeed > -1:
40 --rndSeed $rndSeed
41 #end if
42
43 --out output;
44 ]]></command>
45 <inputs>
46 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
47 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
48 <param label="length of reads to be simulated" name="read_length" type="integer" value="100"/>
49 <param label="amplicon sequencing simulation" name="amplicon" type="boolean" truevalue="--amplicon" falsevalue="" />
50
51 <conditional name="generate">
52 <param name="choice" type="select" label="Type of data to generate">
53 <option value="single_end">Single-End</option>
54 <option value="paired_end">Paired-End</option>
55 <option value="mate_pair">Mate-Pair</option>
56 </param>
57 <when value="single_end">
58 </when>
59 <when value="paired_end">
60 <expand macro="frag_len_sd" />
61 </when>
62 <when value="mate_pair">
63 <expand macro="frag_len_sd" />
64 </when>
65 </conditional>
66
67 <expand macro="aln" />
68 <expand macro="sam" />
69
70 <param label="the first-read insertion rate" help="(--insRate)" name="insRate" type="float" value="0.00009" />
71 <param label="the second-read insertion rate" help="(--insRate2)" name="insRate2" type="float" value="0.00015" />
72 <param label="the first-read deletion rate" help="(--delRate)" name="delRate" type="float" value="0.00011" />
73 <param label="the second-read deletion rate" help="(--delRate2)" name="delRate2" type="float" value="0.00023" />
74
75 <expand macro="rndSeed" />
76 <!-- todo: id, errfree, masN, qShift(2), sepProf -->
77 </inputs>
78 <outputs>
79 <!-- Single End -->
80 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of Illumina sequencing of $input_seq_file.name">
81 <filter>generate['choice'] == "single_end"</filter>
82 </data>
83
84 <!-- Paired End -->
85 <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Forward)">
86 <filter>generate['choice'] != "single_end"</filter>
87 </data>
88 <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Reverse)">
89 <filter>generate['choice'] != "single_end"</filter>
90 </data>
91 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated Illumina data to $input_seq_file.name">
92 <filter>sam</filter>
93 </data>
94
95 <!-- Single End -->
96 <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
97 <filter>aln and generate['choice'] == "single_end"</filter>
98 </data>
99
100 <!-- paired end -->
101 <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
102 <filter>aln and generate['choice'] != "single_end"</filter>
103 </data>
104 <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
105 <filter>aln and generate['choice'] != "single_end"</filter>
106 </data>
107 </outputs>
108 <tests>
109 <test>
110 <param name="rndSeed" value="42" />
111 <param name="input_seq_file" value="input.fa" />
112 <param name="fold_coverage" value="20" />
113 <param name="read_length" value="200" />
114 <param name="choice" value="single_end" />
115 <param name="aln" value="True" />
116 <param name="sam" value="True" />
117
118 <output name="output_fq1_single" file="art.illumina.01.fq" />
119 <output name="output_aln1_single" file="art.illumina.01.aln" lines_diff="2"/>
120 <output name="output_sam" file="art.illumina.01.sam" lines_diff="2"/>
121 </test>
122 <test>
123 <param name="rndSeed" value="42" />
124 <param name="input_seq_file" value="input.fa" />
125 <param name="fold_coverage" value="20" />
126 <param name="read_length" value="200" />
127 <param name="choice" value="paired_end" />
128 <param name="fragment_size" value="300" />
129 <param name="fragment_sd" value="10" />
130 <param name="aln" value="True" />
131 <param name="sam" value="True" />
132
133 <output name="output_fq1_paired" file="art.illumina.021.fq" />
134 <output name="output_fq2_paired" file="art.illumina.022.fq" />
135 <output name="output_aln1_paired" file="art.illumina.021.aln" lines_diff="2"/>
136 <output name="output_aln2_paired" file="art.illumina.022.aln" lines_diff="2"/>
137 <output name="output_sam" file="art.illumina.02.sam" lines_diff="2"/>
138 </test>
139 </tests>
140 <help><![CDATA[
141 Art Illumina Simulator
142 ======================
143
144 ART (art_Illumina Q version) is a simulation program to generate sequence read
145 data of Illumina sequencers. ART generates reads according to the empirical
146 read quality profile summarized from large real read data. ART has been using
147 for testing or benchmarking a variety of methods or tools for next-generation
148 sequencing data analysis, including read alignment, de novo assembly, detection
149 of SNP, CNV, or other structure variation.
150
151 art_Illumina can generate single-end, paired-end, mate-pair reads, and
152 amplicon sequencing simulation of Illumina sequencing platform. Its outputs
153 include FASTQ read, ALN and/or SAM alignment files.
154
155 ]]></help>
156 <expand macro="citation" />
157 </tool>
158