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comparison shovill.xml @ 4:d9f6a00b6db7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
author iuc
date Sun, 25 Aug 2019 05:14:31 -0400
parents 865119fcb694
children 8d1af5db538d
comparison
equal deleted inserted replaced
3:865119fcb694 4:d9f6a00b6db7
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="&gt;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[