Previous changeset 6:83ead2be47b2 (2020-07-02) Next changeset 8:ad80238462c1 (2022-09-16) |
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074" |
modified:
shovill.xml |
b |
diff -r 83ead2be47b2 -r 2a9baa0c4316 shovill.xml --- a/shovill.xml Thu Jul 02 08:58:03 2020 -0400 +++ b/shovill.xml Thu Feb 03 20:41:04 2022 +0000 |
[ |
@@ -1,5 +1,8 @@ -<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0"> +<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1"> <description>Faster SPAdes assembly of Illumina reads</description> + <xrefs> + <xref type="bio.tools">shovill</xref> + </xrefs> <macros> <token name="@TOOL_VERSION@">1.1.0</token> </macros> @@ -8,16 +11,29 @@ </requirements> <version_command>shovill --version</version_command> <command detect_errors="exit_code"><![CDATA[ + ## NOTE: the wrapper uses cp instead of ln -s because of this problem + ## with shovill 1.1.0: https://github.com/tseemann/shovill/issues/157 + #if str($library.lib_type) == "paired" #set r1_ext = $library.R1.extension #set r2_ext = $library.R2.extension - ln -s '$library.R1' fastq_r1.'$r1_ext' && - ln -s '$library.R2' fastq_r2.'$r2_ext' && + #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2' + cp '$library.R1' fastq_r1.'$r1_ext' && + cp '$library.R2' fastq_r2.'$r2_ext' && + #else + ln -s '$library.R1' fastq_r1.'$r1_ext' && + ln -s '$library.R2' fastq_r2.'$r2_ext' && + #end if #else if str($library.lib_type) == "collection" #set r1_ext = $library.input1.forward.extension #set r2_ext = $library.input1.reverse.extension - ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && - ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && + #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2' + cp '$library.input1.forward' fastq_r1.'$r1_ext' && + cp '$library.input1.reverse' fastq_r2.'$r2_ext' && + #else + ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && + ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && + #end if #end if ## Sets the memory used by Shovill according to the following conditions @@ -209,8 +225,8 @@ </test> <test> <!-- Test 6: Gzipped input with trimming --> <param name="lib_type" value="paired" /> - <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" /> - <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" /> + <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" /> + <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" /> <param name="trim" value="true" /> <output name="contigs" ftype="fasta"> <assert_contents> |