Mercurial > repos > devteam > fastqc

annotate rgFastQC.xml @ 21:e7b2202befea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8c357db3dc0861b61f04c7d9f70c5e170e70daa4
author iuc
date Fri, 24 May 2019 13:14:52 -0400
parents ddf5c37952ac
children 3d0c7bdf12f5
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1 <tool id="fastqc" name="FastQC" version="0.72+galaxy1">
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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="0.11.8">fastqc</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="FastQC returned non zero exit code" />
ddf5c37952ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 89976e27bd11f1da3c95a5df6b67297496a8a89b
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8 <exit_code range=":-1" level="fatal" description="FastQC returned non zero exit code" />
ddf5c37952ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 89976e27bd11f1da3c95a5df6b67297496a8a89b
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9 <regex match="There is insufficient memory for the Java Runtime Environment"
ddf5c37952ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 89976e27bd11f1da3c95a5df6b67297496a8a89b
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10 source="stdout"
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11 level="fatal_oom"
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12 description="Out of memory error occurred" />
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13 </stdio>
ddf5c37952ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 89976e27bd11f1da3c95a5df6b67297496a8a89b
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14 <command><![CDATA[
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15 #import re
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16 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
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18 #if $input_file.ext.endswith('.gz'):
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19 #set input_file_sl = $input_name + '.gz'
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20 #elif $input_file.ext.endswith('.bz2'):
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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21 #set input_file_sl = $input_name + '.bz2'
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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22 #else
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23 #set input_file_sl = $input_name
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24 #end if
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26 #if 'bam' in $input_file.ext:
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27 #set format = 'bam'
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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28 #elif 'sam' in $input_file.ext:
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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29 #set format = 'sam'
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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30 #else
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31 #set format = 'fastq'
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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32 #end if
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34 ln -s '${input_file}' '${input_file_sl}' &&
2b0c9d9fc6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
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35 mkdir -p '${html_file.files_path}' &&
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36 fastqc
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37 --outdir '${html_file.files_path}'
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38 #if $contaminants.dataset and str($contaminants) > ''
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39 --contaminants '${contaminants}'
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40 #end if
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41
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42 #if $adapters.dataset and str($adapters) > ''
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43 --adapters '${adapters}'
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44 #end if
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45
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46 #if $limits.dataset and str($limits) > ''
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47 --limits '${limits}'
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48 #end if
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49
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50 --quiet
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51 --extract
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52 #if $min_length:
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53 --min_length $min_length
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54 #end if
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55 $nogroup
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56 --kmers $kmers
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57 -f '${format}'
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58 '${input_file_sl}'
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59
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60 && cp '${html_file.files_path}'/*/fastqc_data.txt output.txt
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61 && cp '${html_file.files_path}'/*\.html output.html
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62
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63 ]]></command>
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64 <inputs>
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65 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
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66 label="Short read data from your current history" />
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67 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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68 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
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69 <param argument="--adapters" type="data" format="tabular" optional="true" label="Adapter list"
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70 help="list of adapters adapter sequences which will be explicity searched against the library. tab delimited file with 2 columns: name and sequence." />
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71 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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72 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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73 <param argument="--nogroup" type="boolean" truevalue="--nogroup" falsevalue="" checked="False"
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74 label="Disable grouping of bases for reads >50bp" help="Using this option will cause fastqc to crash and burn if you use it on really long reads, and your plots may end up a ridiculous size. You have been warned!"/>
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75 <param argument="--min_length" type="integer" value="" optional="true"
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76 label="Lower limit on the length of the sequence to be shown in the report"
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77 help=" As long as you set this to a value greater or equal to your longest read length then this will be the sequence length used to create your read groups. This can be useful for making directly comaparable statistics from datasets with somewhat variable read lengths."/>
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78 <param argument="--kmers" type="integer" value="7" min="2" max="10"
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79 label="length of Kmer to look for" help="note: the Kmer test is disabled and needs to be enabled using a custom Submodule and limits file"/>
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80 </inputs>
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81 <outputs>
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82 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />
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83 <data format="txt" name="text_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" />
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="input_file" value="1000trimmed.fastq" />
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88 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="2"/>
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89 <output name="text_file" file="fastqc_data.txt" ftype="txt"/>
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90 </test>
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91 <test>
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92 <param name="input_file" value="1000trimmed.fastq" />
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93 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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94 <output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="2"/>
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95 <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/>
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96 </test>
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97 <test>
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98 <param name="input_file" value="1000trimmed.fastq" />
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99 <param name="adapters" value="fastqc_adapters.txt" ftype="tabular" />
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100 <output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="2"/>
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101 <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/>
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102 </test>
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103 <test>
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104 <param name="input_file" value="1000trimmed.fastq" />
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105 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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106 <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="2"/>
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107 <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/>
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108 </test>
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109 <test>
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110 <param name="input_file" value="1000trimmed.fastq" ftype="fastq" />
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111 <param name="kmers" value="3" />
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112 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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113 <output name="html_file" file="fastqc_report_kmer.html" ftype="html" lines_diff="2"/>
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114 <output name="text_file" file="fastqc_data_kmer.txt" ftype="txt"/>
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115 <assert_command>
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116 <has_text text="--kmers 3"/>
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117 </assert_command>
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118 </test>
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119 <test>
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120 <param name="input_file" value="1000trimmed.fastq" />
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121 <param name="min_length" value="108" />
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122 <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/>
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123 <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/>
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124 </test>
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125 <test>
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126 <param name="input_file" value="1000trimmed.fastq" ftype="fastq" />
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127 <param name="nogroup" value="--nogroup" />
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128 <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="2"/>
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129 <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/>
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130 <assert_command>
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131 <has_text text="--nogroup"/>
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132 </assert_command>
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133 </test>
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134 <test>
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135 <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
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136 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="2"/>
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137 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt"/>
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138 </test>
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139 </tests>
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140 <help><![CDATA[
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141 .. class:: infomark
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142
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143 **Purpose**
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144
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145 FastQC aims to provide a simple way to do some quality control checks on raw
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146 sequence data coming from high throughput sequencing pipelines.
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147 It provides a set of analyses which you can use to get a quick
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148 impression of whether your data has any problems of
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149 which you should be aware before doing any further analysis.
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150
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151 The main functions of FastQC are:
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152
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153 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
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154 - Providing a quick overview to tell you in which areas there may be problems
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155 - Summary graphs and tables to quickly assess your data
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156 - Export of results to an HTML based permanent report
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157 - Offline operation to allow automated generation of reports without running the interactive application
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158
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159 -----
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160
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161 .. class:: infomark
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162
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163 **FastQC**
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164
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165 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
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166 Kindly acknowledge it as well as this tool if you use it.
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167 FastQC incorporates the Picard-tools_ libraries for SAM/BAM processing.
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168
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169 The contaminants file parameter was borrowed from the independently developed
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170 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
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171 Adaption to version 0.11.2 by T. McGowan.
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172
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173 -----
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174
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175 .. class:: infomark
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176
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177 **Inputs and outputs**
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178
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179 FastQC_ is the best place to look for documentation - it's very good.
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180 A summary follows below for those in a tearing hurry.
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181
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182 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
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183 It will also take an optional file containing a list of contaminants information, in the form of
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184 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
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185 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
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186 which modules to include in the output.
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187
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188 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
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189
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190 - Basic Statistics
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191 - Per base sequence quality
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192 - Per sequence quality scores
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193 - Per base sequence content
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194 - Per base GC content
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195 - Per sequence GC content
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196 - Per base N content
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197 - Sequence Length Distribution
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198 - Sequence Duplication Levels
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199 - Overrepresented sequences
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200 - Kmer Content
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201
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202 All except Basic Statistics and Overrepresented sequences are plots.
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203 .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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204 .. _Picard-tools: https://broadinstitute.github.io/picard/
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205 ]]></help>
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206 <citations>
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207 <citation type="bibtex">
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208 @unpublished{andrews_s,
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209 author = {Andrews, S.},
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210 keywords = {bioinformatics, ngs, qc},
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211 priority = {2},
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212 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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213 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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214 }
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215 </citation>
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216 </citations>
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217 </tool>