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Changeset 3:865119fcb694 (2018-11-13)

Previous changeset 2:f698c7604b3b (2018-10-17) Next changeset 4:d9f6a00b6db7 (2019-08-25)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33

modified:
shovill.xml

diff -r f698c7604b3b -r 865119fcb694 shovill.xml
--- a/shovill.xml Wed Oct 17 11:43:35 2018 -0400
+++ b/shovill.xml Tue Nov 13 10:41:12 2018 -0500

[

b'@@ -1,7 +1,7 @@\n-<tool id="shovill" name="Shovill" version="0.9.0">\n+<tool id="shovill" name="Shovill" version="1.0.4">\n <description>Faster SPAdes assembly of Illumina reads</description>\n <requirements>\n- <requirement type="package" version="0.9.0">shovill</requirement>\n+ <requirement type="package" version="1.0.4">shovill</requirement>\n </requirements>\n <version_command>shovill --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n@@ -31,7 +31,7 @@\n $adv.nocorr\n --minlen $adv.minlen\n --mincov $adv.mincov\n- --asm $adv.asm\n+ --assembler $assembler\n \n ]]></command>\n <inputs>\n@@ -50,6 +50,12 @@\n </conditional>\n <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />\n <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />\n+ <param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades">\n+ <option value="skesa">skesa</option>\n+ <option value="megahit">megahit</option>\n+ <option value="velvet">velvet</option>\n+ <option value="spades" selected="true">Spades</option>\n+ </param>\n <section name="adv" title="Advanced options" expanded="False">\n <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in \'printf\' style (default: \'contig%05d\')" >\n <sanitizer>\n@@ -68,16 +74,11 @@\n <param name="nocorr" argument="--nocorr" type="boolean" truevalue="--nocorr" falsevalue="" checked="True" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)" />\n <param name="minlen" argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" />\n <param name="mincov" argument="--mincov" type="integer" value="2" label="Minimum contig coverage" help="Minimum coverage to call part of a contig. 0 is AUTO (default: 2)" />\n- <param name="asm" argument="--asm" type="select" label="Spades result to correct" help="Which SPAdes output to correct for: before_rr, contigs or scaffolds. (default: \'contigs\')">\n- <option value="before_rr">before_rr</option>\n- <option value="contigs" selected="true">contigs</option>\n- <option value="scaffolds">scaffolds</option>\n- </param>\n </section>\n </inputs>\n \n <outputs>\n- <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" >\n+ <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" >\n <filter>log</filter>\n </data>\n <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>\n@@ -85,7 +86,7 @@\n </outputs>\n \n <tests>\n- <test> \n+ <test> \n <param name="lib_type" value="paired" />\n <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />\n <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />\n@@ -96,17 +97,14 @@\n </output>\n <output name="shovill_std_log" ftype="txt" >\n <assert_contents>\n- <has_text text="Running: seqtk"/>\n- <has_text text="Running: kmc"/>\n- <has_text text="Running: lighter"/>\n- <has_text text="User'..b'e."/>\n+ <has_text text="[mash] Writing to"/>\n+ <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/>\n+ <has_text text="[lighter] Processed 24960 reads:"/>\n+ <has_text text="[FLASH] FLASH v1.2.11 complete!"/>\n+ <has_text text="[spades] ======= SPAdes pipeline finished."/>\n+ <has_text text="[bwa+samtools-sort] [samclip] Done."/>\n+ <has_text text="[pilon] Mean total coverage:"/>\n+ <has_text text="[shovill] Done."/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test> \n+ <param name="lib_type" value="paired" />\n+ <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />\n+ <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />\n+ <param name="assembler" value="megahit" />\n+ <output name="contigs" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">contig00001"/>\n+ </assert_contents>\n+ </output>\n+ <output name="shovill_std_log" ftype="txt" >\n+ <assert_contents>\n+ <has_text text="[mash]"/>\n+ <has_text text="[lighter] Processed 24960 reads"/>\n+ <has_text text="[FLASH] FLASH v1.2.11 complete!"/>\n+ <has_text text="[megahit] --- [STAT]"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test> \n+ <param name="lib_type" value="paired" />\n+ <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />\n+ <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />\n+ <param name="assembler" value="skesa" />\n+ <output name="contigs" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">contig00001"/>\n+ </assert_contents>\n+ </output>\n+ <output name="shovill_std_log" ftype="txt" >\n+ <assert_contents>\n+ <has_text text="[mash]"/>\n+ <has_text text="[lighter] Processed 24960 reads"/>\n+ <has_text text="[FLASH] FLASH v1.2.11 complete!"/>\n+ <has_text text="[skesa] DONE"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test> \n+ <param name="lib_type" value="paired" />\n+ <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />\n+ <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />\n+ <param name="assembler" value="velvet" />\n+ <output name="contigs" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">contig00001"/>\n+ </assert_contents>\n+ </output>\n+ <output name="shovill_std_log" ftype="txt" >\n+ <assert_contents>\n+ <has_text text="[mash]"/>\n+ <has_text text="[lighter] Processed 24960 reads"/>\n+ <has_text text="[FLASH] FLASH v1.2.11 complete!"/>\n+ <has_text text="[velvetg] Final graph has"/>\n </assert_contents>\n </output>\n </test>\n@@ -147,6 +200,7 @@\n - Takes paired end Illumina fastq reads\n - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)\n - Output log file: If set to "Yes", tool will return Shovill\'s log file as part of the output\n+ - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default.\n \n Advanced options:\n - Name format: Format of output contig FASTA IDs in \'printf\' style (default: \'contig%05d\')\n'