Mercurial > repos > bgruening > sailfish
comparison sailfish.xml @ 0:2306a9c40c37 draft
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author | bgruening |
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date | Sat, 12 Jul 2014 03:28:47 -0400 |
parents | |
children | 8792dd3c72b6 |
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-1:000000000000 | 0:2306a9c40c37 |
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1 <tool id="sailfish" name="Sailfish" version="0.6.3.0"> | |
2 <description>transcript quantification from RNA-seq data</description> | |
3 <version_command>sailfish -version</version_command> | |
4 <expand macro="requirements" /> | |
5 <command> | |
6 <![CDATA[ | |
7 sailfish quant -i $index_dir | |
8 #if $single_or_paired-single_or_paired_opts == 'single': | |
9 -l "TYPE=SE" | |
10 -r $single_or_paired_opts.input_singles | |
11 #else: | |
12 -1 $single_or_paired_opts.input_mate1 | |
13 -2 $single_or_paired_opts.input_mate2 | |
14 #if $single_or_paired_opts.orientation == "same": | |
15 -l "TYPE=PE:O=>>" | |
16 #elif $single_or_paired_opts.orientation == "away": | |
17 -l "TYPE=PE:O=<>" | |
18 #else: | |
19 -l "TYPE=PE:O=><" | |
20 #end if | |
21 #end if | |
22 -o <quant_dir> | |
23 | |
24 ]]> | |
25 </command> | |
26 <expand macro="stdio" /> | |
27 <inputs> | |
28 <conditional name="single_or_paired"> | |
29 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> | |
30 <option value="single">Single-end</option> | |
31 <option value="paired">Paired-end</option> | |
32 </param> | |
33 <when value="single"> | |
34 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." /> | |
35 </when> | |
36 <when value="paired"> | |
37 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." /> | |
38 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." /> | |
39 <param name="orientation" type="select" label="Relative orientation of reads within a pair"> | |
40 <option value="same">Mates are oriented in the same direction</option> | |
41 <option value="away">Mates are oriented away from each other</option> | |
42 <option value="toward" selected="True">Mates are oriented toward each other</option> | |
43 </param> | |
44 </when> | |
45 </conditional> | |
46 | |
47 <expand macro="input_conditional_index" /> | |
48 | |
49 </inputs> | |
50 <outputs> | |
51 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> | |
52 <expand macro="output_change_format" /> | |
53 </data> | |
54 </outputs> | |
55 <tests> | |
56 </tests> | |
57 <help> | |
58 <![CDATA[ | |
59 **What it does** | |
60 | |
61 | |
62 The first option >> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is | |
63 upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa. | |
64 | |
65 The second option <> denotes that the mates are oriented away from each other. This implies that start | |
66 of mate1 is closer to start of mate 2 than the end of mate 2, etc. | |
67 | |
68 The third option >< is, perhaps, the most common relative orientation. It denotes that the mates are | |
69 oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa. | |
70 | |
71 ------- | |
72 | |
73 **References** | |
74 | |
75 If you use this Galaxy tool in work leading to a scientific publication please | |
76 cite the following: | |
77 | |
78 | |
79 ]]> | |
80 </help> | |
81 </tool> |