Mercurial > repos > devteam > fastqc

annotate rgFastQC.xml @ 14:da652f6f84cc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 9a987a679243f52297c465180da0bb557a3d0fa7
author iuc
date Sun, 14 Jan 2018 09:31:33 -0500
parents 7d8c56e1a3aa
children d44f3c8ed647
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da652f6f84cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 9a987a679243f52297c465180da0bb557a3d0fa7
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1 <tool id="fastqc" name="FastQC" version="0.71">
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2 <description>Read Quality reports</description>
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3 <requirements>
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4 <requirement type="package" version="0.11.6">fastqc</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #import re
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8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
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10 #if $input_file.ext.endswith('.gz'):
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11 #set input_file_sl = $input_name + '.gz'
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12 #elif $input_file.ext.endswith('.bz2'):
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13 #set input_file_sl = $input_name + '.bz2'
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14 #else
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15 #set input_file_sl = $input_name
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16 #end if
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18 #if 'bam' in $input_file.ext:
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19 #set format = 'bam'
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20 #elif 'sam' in $input_file.ext:
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21 #set format = 'sam'
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22 #else
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23 #set format = 'fastq'
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24 #end if
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26 ln -s '${input_file}' '${input_file_sl}' &&
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27 mkdir -p '${html_file.files_path}' &&
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28 fastqc
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29 --outdir '${html_file.files_path}'
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30
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31 #if $contaminants.dataset and str($contaminants) > ''
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32 --contaminants '${contaminants}'
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33 #end if
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34
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35 #if $limits.dataset and str($limits) > ''
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36 --limits '${limits}'
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37 #end if
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39 --quiet
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40 --extract
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41 -f '${format}'
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42 '${input_file_sl}'
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44 && cp '${html_file.files_path}'/*/fastqc_data.txt output.txt
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45 && cp '${html_file.files_path}'/*\.html output.html
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46
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47 ]]></command>
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48 <inputs>
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49 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
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50 label="Short read data from your current history" />
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51 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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52 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
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53 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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54 help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
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55 </inputs>
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56 <outputs>
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57 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />
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58 <data format="txt" name="text_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input_file" value="1000gsample.fastq" />
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63 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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64 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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65 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
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66 </test>
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67 <test>
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68 <param name="input_file" value="1000gsample.fastq" />
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69 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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70 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
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71 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="4"/>
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72 </test>
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73 <test>
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74 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
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75 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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76 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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77 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
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78 </test>
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79 <test>
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80 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
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81 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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82 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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83 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
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84 </test>
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85 <test>
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86 <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
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87 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/>
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88 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/>
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89 </test>
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90 </tests>
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91 <help>
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92 .. class:: infomark
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93
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94 **Purpose**
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95
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96 FastQC aims to provide a simple way to do some quality control checks on raw
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97 sequence data coming from high throughput sequencing pipelines.
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98 It provides a modular set of analyses which you can use to give a quick
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99 impression of whether your data has any problems of
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100 which you should be aware before doing any further analysis.
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101
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102 The main functions of FastQC are:
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103
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104 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
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105 - Providing a quick overview to tell you in which areas there may be problems
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106 - Summary graphs and tables to quickly assess your data
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107 - Export of results to an HTML based permanent report
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108 - Offline operation to allow automated generation of reports without running the interactive application
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109
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110 -----
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111
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112 .. class:: infomark
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113
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114 **FastQC**
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115
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116 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
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117 Kindly acknowledge it as well as this tool if you use it.
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118 FastQC incorporates the Picard-tools_ libraries for SAM/BAM processing.
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119
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120 The contaminants file parameter was borrowed from the independently developed
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121 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
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122 Adaption to version 0.11.2 by T. McGowan.
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123
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124 -----
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125
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126 .. class:: infomark
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127
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128 **Inputs and outputs**
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129
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130 FastQC_ is the best place to look for documentation - it's very good.
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131 A summary follows below for those in a tearing hurry.
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132
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133 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
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134 It will also take an optional file containing a list of contaminants information, in the form of
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135 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
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136 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
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137 which modules to include in the output.
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138
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139 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
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140
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141 - Basic Statistics
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142 - Per base sequence quality
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143 - Per sequence quality scores
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144 - Per base sequence content
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145 - Per base GC content
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146 - Per sequence GC content
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147 - Per base N content
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148 - Sequence Length Distribution
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149 - Sequence Duplication Levels
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150 - Overrepresented sequences
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151 - Kmer Content
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152
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153 All except Basic Statistics and Overrepresented sequences are plots.
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154 .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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155 .. _Picard-tools: https://broadinstitute.github.io/picard/
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156 </help>
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157 <citations>
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158 <citation type="bibtex">
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159 @unpublished{andrews_s,
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160 author = {Andrews, S.},
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161 keywords = {bioinformatics, ngs, qc},
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162 priority = {2},
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163 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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164 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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165 }
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166 </citation>
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167 </citations>
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168 </tool>