Mercurial > repos > iuc > art
comparison art_solid.xml @ 4:531ff1d417b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author | iuc |
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date | Fri, 07 Sep 2018 10:57:50 -0400 |
parents | bb7e0ccc0029 |
children | ff8599e52a55 |
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3:bb7e0ccc0029 | 4:531ff1d417b6 |
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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 |