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comparison rgFastQC.xml @ 19:9568da3ecb00 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 13:14:29 -0400
parents 7d3cef9c42ca
children 5b63f9c6c831
comparison
equal deleted inserted replaced
18:7d3cef9c42ca 19:9568da3ecb00
83 <data format="txt" name="text_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" /> 83 <data format="txt" name="text_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" />
84 </outputs> 84 </outputs>
85 <tests> 85 <tests>
86 <test> 86 <test>
87 <param name="input_file" value="1000trimmed.fastq" /> 87 <param name="input_file" value="1000trimmed.fastq" />
88 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> 88 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="2"/>
89 <output name="text_file" file="fastqc_data.txt" ftype="txt"/> 89 <output name="text_file" file="fastqc_data.txt" ftype="txt"/>
90 </test> 90 </test>
91 <test> 91 <test>
92 <param name="input_file" value="1000trimmed.fastq" /> 92 <param name="input_file" value="1000trimmed.fastq" />
93 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> 93 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
94 <output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="100"/> 94 <output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="2"/>
95 <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/> 95 <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/>
96 </test> 96 </test>
97 <test> 97 <test>
98 <param name="input_file" value="1000trimmed.fastq" /> 98 <param name="input_file" value="1000trimmed.fastq" />
99 <param name="adapters" value="fastqc_adapters.txt" ftype="tabular" /> 99 <param name="adapters" value="fastqc_adapters.txt" ftype="tabular" />
100 <output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="100"/> 100 <output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="2"/>
101 <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/> 101 <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/>
102 </test> 102 </test>
103 <test> 103 <test>
104 <param name="input_file" value="1000trimmed.fastq" /> 104 <param name="input_file" value="1000trimmed.fastq" />
105 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> 105 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
106 <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="100"/> 106 <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="2"/>
107 <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/> 107 <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/>
108 </test> 108 </test>
109 <test> 109 <test>
110 <param name="input_file" value="1000trimmed.fastq" ftype="fastq" /> 110 <param name="input_file" value="1000trimmed.fastq" ftype="fastq" />
111 <param name="kmers" value="3" /> 111 <param name="kmers" value="3" />
112 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> 112 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
113 <output name="html_file" file="fastqc_report_kmer.html" ftype="html" lines_diff="100"/> 113 <output name="html_file" file="fastqc_report_kmer.html" ftype="html" lines_diff="2"/>
114 <output name="text_file" file="fastqc_data_kmer.txt" ftype="txt"/> 114 <output name="text_file" file="fastqc_data_kmer.txt" ftype="txt"/>
115 <assert_command> 115 <assert_command>
116 <has_text text="--kmers 3"/> 116 <has_text text="--kmers 3"/>
117 </assert_command> 117 </assert_command>
118 </test> 118 </test>
119 <test> 119 <test>
120 <param name="input_file" value="1000trimmed.fastq" /> 120 <param name="input_file" value="1000trimmed.fastq" />
121 <param name="min_length" value="108" /> 121 <param name="min_length" value="108" />
122 <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="100"/> 122 <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/>
123 <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/> 123 <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/>
124 </test> 124 </test>
125 <test> 125 <test>
126 <param name="input_file" value="1000trimmed.fastq" ftype="fastq" /> 126 <param name="input_file" value="1000trimmed.fastq" ftype="fastq" />
127 <param name="nogroup" value="--nogroup" /> 127 <param name="nogroup" value="--nogroup" />
128 <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="100"/> 128 <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="2"/>
129 <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/> 129 <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/>
130 <assert_command> 130 <assert_command>
131 <has_text text="--nogroup"/> 131 <has_text text="--nogroup"/>
132 </assert_command> 132 </assert_command>
133 </test> 133 </test>
134 <test> 134 <test>
135 <param name="input_file" value="hisat_output_1.bam" ftype="bam" /> 135 <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
136 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/> 136 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="2"/>
137 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt"/> 137 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt"/>
138 </test> 138 </test>
139 </tests> 139 </tests>
140 <help><![CDATA[ 140 <help><![CDATA[
141 .. class:: infomark 141 .. class:: infomark