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comparison art_solid.xml @ 4:531ff1d417b6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 10:57:50 -0400
parents bb7e0ccc0029
children ff8599e52a55
comparison
equal deleted inserted replaced
3:bb7e0ccc0029 4:531ff1d417b6
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command><![CDATA[ 8 <command><![CDATA[
9 art_SOLiD 9 art_SOLiD
10 10
11 $sam 11 $sam
12 12
13 #if $rndSeed and $rndSeed > -1: 13 #if $rndSeed and $rndSeed > -1:
14 -r $rndSeed 14 -r $rndSeed
15 #end if 15 #end if
16 16
17 #if $generate.amplicon.use_amplicon == "amplicon_true": 17 #if $generate.amplicon.use_amplicon == "amplicon_true":
18 -A 18 -A
19
20 #if $generate.choice == "single_end":
21 s
22 #else if $generate.choice == "paired_end":
23 p
24 #else:
25 m
26 #end if
27
28 #end if
29
30 '$input_seq_file'
31 output
19 32
20 #if $generate.choice == "single_end": 33 #if $generate.choice == "single_end":
21 s 34 $generate.LEN_READ
35 $fold_coverage
22 #else if $generate.choice == "paired_end": 36 #else if $generate.choice == "paired_end":
23 p 37 $generate.LEN_READ_F3
38 $generate.LEN_READ_F5
39 $fold_coverage
40 $generate.fragment_size
41 $generate.fragment_sd
24 #else: 42 #else:
25 m 43 $generate.LEN_READ
44 $fold_coverage
45 $generate.fragment_size
46 $generate.fragment_sd
26 #end if 47 #end if
27 48
28 #end if 49 #if $generate.amplicon.use_amplicon == "amplicon_true":
50 #if $generate.choice == "single_end":
51 $generate.amplicon.reads_per_amplicon
52 #else:
53 $generate.amplicon.read_pairs_per_amplicon
54 #end if
55 #end if
29 56
30 $input_seq_file
31 output
32
33 #if $generate.choice == "single_end":
34 $generate.LEN_READ
35 $fold_coverage
36 #else if $generate.choice == "paired_end":
37 $generate.LEN_READ_F3
38 $generate.LEN_READ_F5
39 $fold_coverage
40 $generate.fragment_size
41 $generate.fragment_sd
42 #else:
43 $generate.LEN_READ
44 $fold_coverage
45 $generate.fragment_size
46 $generate.fragment_sd
47 #end if
48
49 #if $generate.amplicon.use_amplicon == "amplicon_true":
50 #if $generate.choice == "single_end":
51 $generate.amplicon.reads_per_amplicon
52 #else:
53 $generate.amplicon.read_pairs_per_amplicon
54 #end if
55 #end if
56 ]]></command> 57 ]]></command>
57 <inputs> 58 <inputs>
58 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> 59 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
59 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> 60 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
60 61