Mercurial > repos > hackdna > fastqc
comparison fastqc_checker.xml @ 0:d8d131d08779 draft default tip
Initial upload.
author | hackdna |
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date | Tue, 21 May 2013 11:48:53 -0400 |
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1 <tool id="fastqc_checker_1" name="FastQC checker" version="1.0.0"> | |
2 <description>for quality control of high throughput sequence data</description> | |
3 | |
4 <command interpreter="python"> | |
5 fastqc_checker.py -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc -o $output $input | |
6 </command> | |
7 | |
8 <inputs> | |
9 <param format="fastq" name="input" type="data" label="Source files" multiple="true"/> | |
10 </inputs> | |
11 <outputs> | |
12 <data format="txt" name="output"/> | |
13 </outputs> | |
14 | |
15 <help> | |
16 | |
17 .. class:: infomark | |
18 | |
19 **Purpose** | |
20 | |
21 FastQC aims to provide a simple way to do some quality control checks on raw | |
22 sequence data coming from high throughput sequencing pipelines. | |
23 It provides a modular set of analyses which you can use to give a quick | |
24 impression of whether your data has any problems of | |
25 which you should be aware before doing any further analysis. | |
26 | |
27 **FastQC documentation** | |
28 | |
29 This is a Galaxy interface to the external package FastQC_. | |
30 Specific documentation on FastQC can be found on that site. | |
31 | |
32 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ | |
33 | |
34 ----- | |
35 | |
36 .. class:: infomark | |
37 | |
38 **Inputs and outputs** | |
39 | |
40 This wrapper will accept one or more fastq files. | |
41 | |
42 The tool produces a single output file that contains summary of all the results, including the following: | |
43 | |
44 - Basic Statistics | |
45 - Per base sequence quality | |
46 - Per sequence quality scores | |
47 - Per base sequence content | |
48 - Per base GC content | |
49 - Per sequence GC content | |
50 - Per base N content | |
51 - Sequence Length Distribution | |
52 - Sequence Duplication Levels | |
53 - Overrepresented sequences | |
54 - Kmer Content | |
55 | |
56 </help> | |
57 </tool> |