annotate tabular_to_fastq.xml @ 0:b334cd1095ea draft

Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:43 -0500
parents
children 92034dcbb40a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0">
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
2 <description>converter</description>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
3 <requirements>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
5 </requirements>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
6 <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
7 <inputs>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
8 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
9 <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
10 <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
11 <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
12 </inputs>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
13 <outputs>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
14 <data name="output_file" format="fastq" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
15 </outputs>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
16 <tests>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
17 <!-- basic test -->
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
18 <test>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
19 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
20 <param name="identifier" value="1" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
21 <param name="sequence" value="2" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
22 <param name="quality" value="3" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
23 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
24 </test>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
25 <!-- color space test -->
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
26 <test>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
27 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
28 <param name="identifier" value="1" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
29 <param name="sequence" value="2" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
30 <param name="quality" value="3" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
31 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
32 </test>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
33 </tests>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
34 <help>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
35 **What it does**
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
36
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
37 This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool.
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
38
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
39 ------
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
40
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
41 **Citation**
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
42
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
43 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
44
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
45
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
46 </help>
b334cd1095ea Imported from capsule None
devteam
parents:
diff changeset
47 </tool>