comparison rgFastQC.xml @ 9:3a458e268066 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e

8:06819360a9e2

<tool id="fastqc" name="FastQC" version="0.66">
    <description>Read Quality reports</description>
    <requirements>
        <requirement type="package" version="0.11.5">fastqc</requirement>
    </requirements>
    <stdio>

            <param name="input_file" value="1000gsample.fastq" />
            <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
            <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
            <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
        </test>
    </tests>
    <help>

.. class:: infomark

impression of whether your data has any problems of
which you should be aware before doing any further analysis.

The main functions of FastQC are:

- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application

**Inputs and outputs**

FastQC_ is the best place to look for documentation - it's very good.
A summary follows below for those in a tearing hurry.

This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check.
It will also take an optional file containing a list of contaminants information, in the form of
a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
limits.txt file that allows setting the warning thresholds for the different modules and also specifies
which modules to include in the output.

9:3a458e268066

<tool id="fastqc" name="FastQC" version="0.67">
    <description>Read Quality reports</description>
    <requirements>
        <requirement type="package" version="0.11.5">fastqc</requirement>
    </requirements>
    <stdio>

            <param name="input_file" value="1000gsample.fastq" />
            <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
            <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
            <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq.gz" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
        </test>
    </tests>
    <help>

.. class:: infomark

impression of whether your data has any problems of
which you should be aware before doing any further analysis.

The main functions of FastQC are:

- Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), 
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application

**Inputs and outputs**

FastQC_ is the best place to look for documentation - it's very good.
A summary follows below for those in a tearing hurry.

This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
It will also take an optional file containing a list of contaminants information, in the form of
a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
limits.txt file that allows setting the warning thresholds for the different modules and also specifies
which modules to include in the output.