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comparison rgFastQC.xml @ 7:ec73b7c83b2c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
author devteam
date Wed, 02 Nov 2016 16:12:38 -0400
parents e8c90ad3cbf9
children 5b995cef2fbb
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6:e8c90ad3cbf9 7:ec73b7c83b2c
1 <tool id="fastqc" name="FastQC" version="0.66"> 1 <tool id="fastqc" name="FastQC" version="0.67">
2 <description>Read Quality reports</description> 2 <description>Read Quality reports</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.11.5">fastqc</requirement> 4 <requirement type="package" version="0.11.5">fastqc</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
46 <param name="input_file" value="1000gsample.fastq" /> 46 <param name="input_file" value="1000gsample.fastq" />
47 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> 47 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
48 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/> 48 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
49 <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/> 49 <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
50 </test> 50 </test>
51 <test>
52 <param name="input_file" value="1000gsample.fastq.gz" />
53 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
54 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
55 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
56 </test>
51 </tests> 57 </tests>
52 <help> 58 <help>
53 59
54 .. class:: infomark 60 .. class:: infomark
55 61
61 impression of whether your data has any problems of 67 impression of whether your data has any problems of
62 which you should be aware before doing any further analysis. 68 which you should be aware before doing any further analysis.
63 69
64 The main functions of FastQC are: 70 The main functions of FastQC are:
65 71
66 - Import of data from BAM, SAM or FastQ files (any variant) 72 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
67 - Providing a quick overview to tell you in which areas there may be problems 73 - Providing a quick overview to tell you in which areas there may be problems
68 - Summary graphs and tables to quickly assess your data 74 - Summary graphs and tables to quickly assess your data
69 - Export of results to an HTML based permanent report 75 - Export of results to an HTML based permanent report
70 - Offline operation to allow automated generation of reports without running the interactive application 76 - Offline operation to allow automated generation of reports without running the interactive application
71 77
92 **Inputs and outputs** 98 **Inputs and outputs**
93 99
94 FastQC_ is the best place to look for documentation - it's very good. 100 FastQC_ is the best place to look for documentation - it's very good.
95 A summary follows below for those in a tearing hurry. 101 A summary follows below for those in a tearing hurry.
96 102
97 This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. 103 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
98 It will also take an optional file containing a list of contaminants information, in the form of 104 It will also take an optional file containing a list of contaminants information, in the form of
99 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom 105 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
100 limits.txt file that allows setting the warning thresholds for the different modules and also specifies 106 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
101 which modules to include in the output. 107 which modules to include in the output.
102 108