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