Mercurial > repos > iuc > shovill
comparison shovill.xml @ 4:d9f6a00b6db7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
author | iuc |
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date | Sun, 25 Aug 2019 05:14:31 -0400 |
parents | 865119fcb694 |
children | 8d1af5db538d |
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3:865119fcb694 | 4:d9f6a00b6db7 |
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1 <tool id="shovill" name="Shovill" version="1.0.4"> | 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> | |
4 <token name="@TOOL_VERSION@">1.0.4</token> | |
5 </macros> | |
3 <requirements> | 6 <requirements> |
4 <requirement type="package" version="1.0.4">shovill</requirement> | 7 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement> |
5 </requirements> | 8 </requirements> |
6 <version_command>shovill --version</version_command> | 9 <version_command>shovill --version</version_command> |
7 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
11 #if str($library.lib_type) == "paired" | |
12 #set r1_ext = $library.R1.extension | |
13 #set r2_ext = $library.R2.extension | |
14 ln -s '$library.R1' fastq_r1.'$r1_ext' && | |
15 ln -s '$library.R2' fastq_r2.'$r2_ext' && | |
16 #else if str($library.lib_type) == "collection" | |
17 #set r1_ext = $library.input1.forward.extension | |
18 #set r2_ext = $library.input1.reverse.extension | |
19 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && | |
20 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && | |
21 #end if | |
22 | |
8 shovill | 23 shovill |
9 --outdir 'out' | 24 --outdir 'out' |
10 --cpus \${GALAXY_SLOTS:-1} | 25 --cpus \${GALAXY_SLOTS:-1} |
11 --ram \${SHOVILL_RAM:-4} | 26 --ram \${SHOVILL_RAM:-4} |
12 #if str($library.lib_type) == "paired" | 27 --R1 fastq_r1.'$r1_ext' |
13 --R1 '$library.R1' | 28 --R2 fastq_r2.'$r2_ext' |
14 --R2 '$library.R2' | |
15 #else if str($library.lib_type) == "collection" | |
16 --R1 '$library.input1.forward' | |
17 --R2 '$library.input1.reverse' | |
18 #end if | |
19 $trim | 29 $trim |
20 --namefmt '$adv.namefmt' | 30 --namefmt '$adv.namefmt' |
21 --depth '$adv.depth' | 31 --depth '$adv.depth' |
22 #if $adv.gsize | 32 #if $adv.gsize |
23 --gsize '$adv.gsize' | 33 --gsize '$adv.gsize' |
96 </assert_contents> | 106 </assert_contents> |
97 </output> | 107 </output> |
98 <output name="shovill_std_log" ftype="txt" > | 108 <output name="shovill_std_log" ftype="txt" > |
99 <assert_contents> | 109 <assert_contents> |
100 <has_text text="[mash]"/> | 110 <has_text text="[mash]"/> |
101 <has_text text="[lighter] Processed 24960 reads"/> | 111 <has_text text="[lighter] Processed 1714 reads"/> |
102 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> | 112 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> |
103 <has_text text="[spades] ======= SPAdes pipeline finished."/> | 113 <has_text text="[spades] ======= SPAdes pipeline finished."/> |
104 </assert_contents> | 114 </assert_contents> |
105 </output> | 115 </output> |
106 </test> | 116 </test> |
123 </output> | 133 </output> |
124 <output name="shovill_std_log" ftype="txt" > | 134 <output name="shovill_std_log" ftype="txt" > |
125 <assert_contents> | 135 <assert_contents> |
126 <has_text text="[mash] Writing to"/> | 136 <has_text text="[mash] Writing to"/> |
127 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/> | 137 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/> |
128 <has_text text="[lighter] Processed 24960 reads:"/> | 138 <has_text text="[lighter] Processed 2000 reads:"/> |
129 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> | 139 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> |
130 <has_text text="[spades] ======= SPAdes pipeline finished."/> | 140 <has_text text="[spades] ======= SPAdes pipeline finished."/> |
131 <has_text text="[bwa+samtools-sort] [samclip] Done."/> | 141 <has_text text="[bwa+samtools-sort] [samclip] Done."/> |
132 <has_text text="[pilon] Mean total coverage:"/> | 142 <has_text text="[pilon] Mean total coverage:"/> |
133 <has_text text="[shovill] Done."/> | 143 <has_text text="[shovill] Done."/> |
145 </assert_contents> | 155 </assert_contents> |
146 </output> | 156 </output> |
147 <output name="shovill_std_log" ftype="txt" > | 157 <output name="shovill_std_log" ftype="txt" > |
148 <assert_contents> | 158 <assert_contents> |
149 <has_text text="[mash]"/> | 159 <has_text text="[mash]"/> |
150 <has_text text="[lighter] Processed 24960 reads"/> | 160 <has_text text="[lighter] Processed 1714 reads"/> |
151 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> | 161 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> |
152 <has_text text="[megahit] --- [STAT]"/> | 162 <has_text_matching expression="\[megahit\] .* ALL DONE"/> |
153 </assert_contents> | 163 </assert_contents> |
154 </output> | 164 </output> |
155 </test> | 165 </test> |
156 <test> <!-- Test 4: Alternate assembler #2: Skesa --> | 166 <test> <!-- Test 4: Alternate assembler #2: Skesa --> |
157 <param name="lib_type" value="paired" /> | 167 <param name="lib_type" value="paired" /> |
164 </assert_contents> | 174 </assert_contents> |
165 </output> | 175 </output> |
166 <output name="shovill_std_log" ftype="txt" > | 176 <output name="shovill_std_log" ftype="txt" > |
167 <assert_contents> | 177 <assert_contents> |
168 <has_text text="[mash]"/> | 178 <has_text text="[mash]"/> |
169 <has_text text="[lighter] Processed 24960 reads"/> | 179 <has_text text="[lighter] Processed 1714 reads"/> |
170 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> | 180 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> |
171 <has_text text="[skesa] DONE"/> | 181 <has_text text="[skesa] DONE"/> |
172 </assert_contents> | 182 </assert_contents> |
173 </output> | 183 </output> |
174 </test> | 184 </test> |
183 </assert_contents> | 193 </assert_contents> |
184 </output> | 194 </output> |
185 <output name="shovill_std_log" ftype="txt" > | 195 <output name="shovill_std_log" ftype="txt" > |
186 <assert_contents> | 196 <assert_contents> |
187 <has_text text="[mash]"/> | 197 <has_text text="[mash]"/> |
188 <has_text text="[lighter] Processed 24960 reads"/> | 198 <has_text text="[lighter] Processed 1714 reads"/> |
189 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> | 199 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> |
190 <has_text text="[velvetg] Final graph has"/> | 200 <has_text text="[velvetg] Final graph has"/> |
201 </assert_contents> | |
202 </output> | |
203 </test> | |
204 <test> <!-- Test 6: Gzipped input with trimming --> | |
205 <param name="lib_type" value="paired" /> | |
206 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" /> | |
207 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" /> | |
208 <param name="trim" value="true" /> | |
209 <output name="contigs" ftype="fasta"> | |
210 <assert_contents> | |
211 <has_text text=">contig00001"/> | |
212 </assert_contents> | |
213 </output> | |
214 <output name="shovill_std_log" ftype="txt" > | |
215 <assert_contents> | |
216 <has_text text="[mash]"/> | |
217 <has_text text="[lighter] Processed 1714 reads"/> | |
218 <has_text text="[FLASH] FLASH v1.2.11 complete!"/> | |
219 <has_text text="[spades] ======= SPAdes pipeline finished."/> | |
191 </assert_contents> | 220 </assert_contents> |
192 </output> | 221 </output> |
193 </test> | 222 </test> |
194 </tests> | 223 </tests> |
195 <help><![CDATA[ | 224 <help><![CDATA[ |