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comparison shovill.xml @ 6:83ead2be47b2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
author iuc
date Thu, 02 Jul 2020 08:58:03 -0400
parents 8d1af5db538d
children 2a9baa0c4316
comparison
equal deleted inserted replaced
5:8d1af5db538d 6:83ead2be47b2
1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0">
2 <description>Faster SPAdes assembly of Illumina reads</description> 2 <description>Faster SPAdes assembly of Illumina reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.4</token> 4 <token name="@TOOL_VERSION@">1.1.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement>
8 </requirements> 8 </requirements>
9 <version_command>shovill --version</version_command> 9 <version_command>shovill --version</version_command>
112 <has_text text="&gt;contig00001"/> 112 <has_text text="&gt;contig00001"/>
113 </assert_contents> 113 </assert_contents>
114 </output> 114 </output>
115 <output name="shovill_std_log" ftype="txt" > 115 <output name="shovill_std_log" ftype="txt" >
116 <assert_contents> 116 <assert_contents>
117 <has_text text="[mash]"/> 117 <has_text text="Read stats: total_bp = 300000"/>
118 <has_text text="[lighter] Processed 1714 reads"/> 118 <has_text text="[lighter] Processed 820 reads"/>
119 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> 119 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
120 <has_text text="[spades] ======= SPAdes pipeline finished."/> 120 <has_text text="[spades] ======= SPAdes pipeline finished."/>
121 </assert_contents> 121 </assert_contents>
122 </output> 122 </output>
123 </test> 123 </test>
138 <has_text text="&gt;contig001"/> 138 <has_text text="&gt;contig001"/>
139 </assert_contents> 139 </assert_contents>
140 </output> 140 </output>
141 <output name="shovill_std_log" ftype="txt" > 141 <output name="shovill_std_log" ftype="txt" >
142 <assert_contents> 142 <assert_contents>
143 <has_text text="[mash] Writing to"/>
144 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/> 143 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/>
145 <has_text text="[lighter] Processed 2000 reads:"/> 144 <has_text text="[lighter] Processed"/>
146 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> 145 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
147 <has_text text="[spades] ======= SPAdes pipeline finished."/> 146 <has_text text="[spades] ======= SPAdes pipeline finished."/>
148 <has_text text="[bwa+samtools-sort] [samclip] Done."/> 147 <has_text text="[bwa+samtools-sort] [samclip] Done."/>
149 <has_text text="[pilon] Mean total coverage:"/> 148 <has_text text="[pilon] Mean total coverage:"/>
150 <has_text text="[shovill] Done."/> 149 <has_text text="[shovill] Done."/>
161 <has_text text="&gt;contig00001"/> 160 <has_text text="&gt;contig00001"/>
162 </assert_contents> 161 </assert_contents>
163 </output> 162 </output>
164 <output name="shovill_std_log" ftype="txt" > 163 <output name="shovill_std_log" ftype="txt" >
165 <assert_contents> 164 <assert_contents>
166 <has_text text="[mash]"/> 165 <has_text text="[lighter] Processed"/>
167 <has_text text="[lighter] Processed 1714 reads"/>
168 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> 166 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
169 <has_text_matching expression="\[megahit\] .* ALL DONE"/> 167 <has_text_matching expression="\[megahit\] .* ALL DONE"/>
168 <has_text text="[shovill] Done."/>
170 </assert_contents> 169 </assert_contents>
171 </output> 170 </output>
172 </test> 171 </test>
173 <test> <!-- Test 4: Alternate assembler #2: Skesa --> 172 <test> <!-- Test 4: Alternate assembler #2: Skesa -->
174 <param name="lib_type" value="paired" /> 173 <param name="lib_type" value="paired" />
180 <has_text text="&gt;contig00001"/> 179 <has_text text="&gt;contig00001"/>
181 </assert_contents> 180 </assert_contents>
182 </output> 181 </output>
183 <output name="shovill_std_log" ftype="txt" > 182 <output name="shovill_std_log" ftype="txt" >
184 <assert_contents> 183 <assert_contents>
185 <has_text text="[mash]"/> 184 <has_text text="[lighter] Processed"/>
186 <has_text text="[lighter] Processed 1714 reads"/>
187 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> 185 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
188 <has_text text="[skesa] DONE"/> 186 <has_text text="[skesa] DONE"/>
187 <has_text text="[shovill] Done."/>
189 </assert_contents> 188 </assert_contents>
190 </output> 189 </output>
191 </test> 190 </test>
192 <test> <!-- Test 5: Alternate assembler #3: Velvet --> 191 <test> <!-- Test 5: Alternate assembler #3: Velvet -->
193 <param name="lib_type" value="paired" /> 192 <param name="lib_type" value="paired" />
199 <has_text text="&gt;contig00001"/> 198 <has_text text="&gt;contig00001"/>
200 </assert_contents> 199 </assert_contents>
201 </output> 200 </output>
202 <output name="shovill_std_log" ftype="txt" > 201 <output name="shovill_std_log" ftype="txt" >
203 <assert_contents> 202 <assert_contents>
204 <has_text text="[mash]"/> 203 <has_text text="[lighter] Processed"/>
205 <has_text text="[lighter] Processed 1714 reads"/>
206 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> 204 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
207 <has_text text="[velvetg] Final graph has"/> 205 <has_text text="[velvetg] Final graph has"/>
206 <has_text text="[shovill] Done."/>
208 </assert_contents> 207 </assert_contents>
209 </output> 208 </output>
210 </test> 209 </test>
211 <test> <!-- Test 6: Gzipped input with trimming --> 210 <test> <!-- Test 6: Gzipped input with trimming -->
212 <param name="lib_type" value="paired" /> 211 <param name="lib_type" value="paired" />
218 <has_text text="&gt;contig00001"/> 217 <has_text text="&gt;contig00001"/>
219 </assert_contents> 218 </assert_contents>
220 </output> 219 </output>
221 <output name="shovill_std_log" ftype="txt" > 220 <output name="shovill_std_log" ftype="txt" >
222 <assert_contents> 221 <assert_contents>
223 <has_text text="[mash]"/> 222 <has_text text="[lighter] Processed"/>
224 <has_text text="[lighter] Processed 1714 reads"/>
225 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> 223 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
226 <has_text text="[spades] ======= SPAdes pipeline finished."/> 224 <has_text text="[spades] ======= SPAdes pipeline finished."/>
225 <has_text text="[shovill] Done."/>
227 </assert_contents> 226 </assert_contents>
228 </output> 227 </output>
229 </test> 228 </test>
230 </tests> 229 </tests>
231 <help><![CDATA[ 230 <help><![CDATA[