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comparison shovill.xml @ 7:2a9baa0c4316 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
author iuc
date Thu, 03 Feb 2022 20:41:04 +0000
parents 83ead2be47b2
children ad80238462c1
comparison
equal deleted inserted replaced
6:83ead2be47b2 7:2a9baa0c4316
1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1">
2 <description>Faster SPAdes assembly of Illumina reads</description> 2 <description>Faster SPAdes assembly of Illumina reads</description>
3 <xrefs>
4 <xref type="bio.tools">shovill</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@TOOL_VERSION@">1.1.0</token> 7 <token name="@TOOL_VERSION@">1.1.0</token>
5 </macros> 8 </macros>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement>
8 </requirements> 11 </requirements>
9 <version_command>shovill --version</version_command> 12 <version_command>shovill --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 ## NOTE: the wrapper uses cp instead of ln -s because of this problem
15 ## with shovill 1.1.0: https://github.com/tseemann/shovill/issues/157
16
11 #if str($library.lib_type) == "paired" 17 #if str($library.lib_type) == "paired"
12 #set r1_ext = $library.R1.extension 18 #set r1_ext = $library.R1.extension
13 #set r2_ext = $library.R2.extension 19 #set r2_ext = $library.R2.extension
14 ln -s '$library.R1' fastq_r1.'$r1_ext' && 20 #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2'
15 ln -s '$library.R2' fastq_r2.'$r2_ext' && 21 cp '$library.R1' fastq_r1.'$r1_ext' &&
22 cp '$library.R2' fastq_r2.'$r2_ext' &&
23 #else
24 ln -s '$library.R1' fastq_r1.'$r1_ext' &&
25 ln -s '$library.R2' fastq_r2.'$r2_ext' &&
26 #end if
16 #else if str($library.lib_type) == "collection" 27 #else if str($library.lib_type) == "collection"
17 #set r1_ext = $library.input1.forward.extension 28 #set r1_ext = $library.input1.forward.extension
18 #set r2_ext = $library.input1.reverse.extension 29 #set r2_ext = $library.input1.reverse.extension
19 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && 30 #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2'
20 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && 31 cp '$library.input1.forward' fastq_r1.'$r1_ext' &&
32 cp '$library.input1.reverse' fastq_r2.'$r2_ext' &&
33 #else
34 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
35 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
36 #end if
21 #end if 37 #end if
22 38
23 ## Sets the memory used by Shovill according to the following conditions 39 ## Sets the memory used by Shovill according to the following conditions
24 ## (1) If SHOVILL_RAM is already set, use this value 40 ## (1) If SHOVILL_RAM is already set, use this value
25 ## (2) Otherwise, set based on GALAXY_MEMORY_MB 41 ## (2) Otherwise, set based on GALAXY_MEMORY_MB
207 </assert_contents> 223 </assert_contents>
208 </output> 224 </output>
209 </test> 225 </test>
210 <test> <!-- Test 6: Gzipped input with trimming --> 226 <test> <!-- Test 6: Gzipped input with trimming -->
211 <param name="lib_type" value="paired" /> 227 <param name="lib_type" value="paired" />
212 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" /> 228 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" />
213 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" /> 229 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" />
214 <param name="trim" value="true" /> 230 <param name="trim" value="true" />
215 <output name="contigs" ftype="fasta"> 231 <output name="contigs" ftype="fasta">
216 <assert_contents> 232 <assert_contents>
217 <has_text text="&gt;contig00001"/> 233 <has_text text="&gt;contig00001"/>
218 </assert_contents> 234 </assert_contents>