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comparison genomescope.xml @ 2:01210c4e9144 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
author iuc
date Thu, 18 Aug 2022 12:50:44 +0000
parents 3169a38c2656
children 460fad600dce
comparison
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1:3169a38c2656 2:01210c4e9144
1 <tool id="genomescope" name="GenomeScope" version="@VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> 1 <tool id="genomescope" name="GenomeScope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01">
2 <description>reference-free genome profiling</description> 2 <description>reference-free genome profiling</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.0</token> 4 <token name="@TOOL_VERSION@">2.0</token>
5 <token name="@SUFFIX_VERSION@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@VERSION@">genomescope2</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">genomescope2</requirement>
9 </requirements> 9 </requirements>
10 <version_command>genomescope2 --version</version_command> 10 <version_command>genomescope2 --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 genomescope2 12 genomescope2
13 --input '$input' 13 --input '$input'
106 <param name="output_files" value="model_output,summary_output,progress_output"/> 106 <param name="output_files" value="model_output,summary_output,progress_output"/>
107 </section> 107 </section>
108 <section name="advanced_options"> 108 <section name="advanced_options">
109 <param name="testing" value="true"/> 109 <param name="testing" value="true"/>
110 </section> 110 </section>
111 <output name="linear_plot" file="genomescope-out1-1.png" ftype="png"/> 111 <output name="linear_plot" ftype="png">
112 <output name="log_plot" file="genomescope-out1-2.png" ftype="png"/> 112 <assert_contents>
113 <output name="transformed_linear_plot" file="genomescope-out1-3.png" ftype="png"/> 113 <has_size value="223370" delta="6000"/>
114 <output name="transformed_log_plot" file="genomescope-out1-4.png" ftype="png" compare="sim_size"/> 114 </assert_contents>
115 </output>
116 <output name="log_plot" ftype="png">
117 <assert_contents>
118 <has_size value="201425" delta="6000"/>
119 </assert_contents>
120 </output>
121 <output name="transformed_linear_plot" ftype="png">
122 <assert_contents>
123 <has_size value="221442" delta="6000"/>
124 </assert_contents>
125 </output>
126 <output name="transformed_log_plot" ftype="png">
127 <assert_contents>
128 <has_size value="210889" delta="6000"/>
129 </assert_contents>
130 </output>
115 <output name="model" file="genomescope-out1-1.txt" ftype="txt" lines_diff="2"/> 131 <output name="model" file="genomescope-out1-1.txt" ftype="txt" lines_diff="2"/>
116 <output name="summary" file="genomescope-out1-2.txt" ftype="txt" lines_diff="2"/> 132 <output name="summary" file="genomescope-out1-2.txt" ftype="txt" lines_diff="2"/>
117 <output name="progress" file="genomescope-out1-3.txt" ftype="txt" lines_diff="2"/> 133 <output name="progress" file="genomescope-out1-3.txt" ftype="txt" lines_diff="2"/>
118 <output name="model_params" file="genomescope-out1-1.tab" ftype="tabular"/> 134 <output name="model_params" file="genomescope-out1-1.tab" ftype="tabular"/>
119 </test> 135 </test>
127 <section name="output_options"> 143 <section name="output_options">
128 <param name="output_files" value="summary_output"/> 144 <param name="output_files" value="summary_output"/>
129 </section> 145 </section>
130 <output name="linear_plot" ftype="png"> 146 <output name="linear_plot" ftype="png">
131 <assert_contents> 147 <assert_contents>
132 <has_size value="223370" delta="300"/> 148 <has_size value="223370" delta="6000"/>
133 </assert_contents> 149 </assert_contents>
134 </output> 150 </output>
135 <output name="log_plot" ftype="png"> 151 <output name="log_plot" ftype="png">
136 <assert_contents> 152 <assert_contents>
137 <has_size value="201425" delta="300"/> 153 <has_size value="201425" delta="6000"/>
138 </assert_contents> 154 </assert_contents>
139 </output> 155 </output>
140 <output name="transformed_linear_plot" ftype="png"> 156 <output name="transformed_linear_plot" ftype="png">
141 <assert_contents> 157 <assert_contents>
142 <has_size value="221442" delta="300"/> 158 <has_size value="221442" delta="6000"/>
143 </assert_contents> 159 </assert_contents>
144 </output> 160 </output>
145 <output name="transformed_log_plot" ftype="png"> 161 <output name="transformed_log_plot" ftype="png">
146 <assert_contents> 162 <assert_contents>
147 <has_size value="210889" delta="300"/> 163 <has_size value="210889" delta="6000"/>
148 </assert_contents> 164 </assert_contents>
149 </output> 165 </output>
150 <output name="summary" ftype="txt" lines_diff="2"> 166 <output name="summary" ftype="txt" lines_diff="2">
151 <assert_contents> 167 <assert_contents>
152 <has_line line="initial repetitiveness = 0.1"/> 168 <has_line line="initial repetitiveness = 0.1"/>
165 <section name="output_options"> 181 <section name="output_options">
166 <param name="output_files" value="summary_output"/> 182 <param name="output_files" value="summary_output"/>
167 </section> 183 </section>
168 <output name="linear_plot" ftype="png"> 184 <output name="linear_plot" ftype="png">
169 <assert_contents> 185 <assert_contents>
170 <has_size value="213366" delta="300"/> 186 <has_size value="213366" delta="6000"/>
171 </assert_contents> 187 </assert_contents>
172 </output> 188 </output>
173 <output name="log_plot" ftype="png"> 189 <output name="log_plot" ftype="png">
174 <assert_contents> 190 <assert_contents>
175 <has_size value="218425" delta="300"/> 191 <has_size value="218425" delta="6000"/>
176 </assert_contents> 192 </assert_contents>
177 </output> 193 </output>
178 <output name="transformed_linear_plot" ftype="png"> 194 <output name="transformed_linear_plot" ftype="png">
179 <assert_contents> 195 <assert_contents>
180 <has_size value="217280" delta="300"/> 196 <has_size value="217280" delta="6000"/>
181 </assert_contents> 197 </assert_contents>
182 </output> 198 </output>
183 <output name="transformed_log_plot" ftype="png"> 199 <output name="transformed_log_plot" ftype="png">
184 <assert_contents> 200 <assert_contents>
185 <has_size value="229021" delta="300"/> 201 <has_size value="229021" delta="6000"/>
186 </assert_contents> 202 </assert_contents>
187 </output> 203 </output>
188 <output name="summary" ftype="txt" lines_diff="2"> 204 <output name="summary" ftype="txt" lines_diff="2">
189 <assert_contents> 205 <assert_contents>
190 <has_line line="initial heterozygosities = 0.04,0.01"/> 206 <has_line line="initial heterozygosities = 0.04,0.01"/>