Mercurial > repos > iuc > shovill
comparison shovill.xml @ 1:57d5928f456e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author | iuc |
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date | Wed, 07 Mar 2018 02:10:01 -0500 |
parents | 196a599ec43d |
children | f698c7604b3b |
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0:196a599ec43d | 1:57d5928f456e |
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1 <tool id="shovill" name="Shovill" version="0.8.0"> | 1 <tool id="shovill" name="Shovill" version="0.9.0"> |
2 <description>Faster SPAdes assembly of Illumina reads</description> | 2 <description>Faster SPAdes assembly of Illumina reads</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.8.0">shovill</requirement> | 4 <requirement type="package" version="0.9.0">shovill</requirement> |
5 </requirements> | 5 </requirements> |
6 <version_command>shovill --version</version_command> | 6 <version_command>shovill --version</version_command> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 shovill | 8 shovill |
9 --outdir 'out' | 9 --outdir 'out' |
30 #end if | 30 #end if |
31 $adv.nocorr | 31 $adv.nocorr |
32 --minlen $adv.minlen | 32 --minlen $adv.minlen |
33 --mincov $adv.mincov | 33 --mincov $adv.mincov |
34 --asm $adv.asm | 34 --asm $adv.asm |
35 | 35 |
36 ]]></command> | 36 ]]></command> |
37 <inputs> | 37 <inputs> |
38 <conditional name="library"> | 38 <conditional name="library"> |
39 <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> | 39 <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> |
40 <option value="paired" selected="true">Paired End</option> | 40 <option value="paired" selected="true">Paired End</option> |
43 <when value="paired"> | 43 <when value="paired"> |
44 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> | 44 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> |
45 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> | 45 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> |
46 </when> | 46 </when> |
47 <when value="collection"> | 47 <when value="collection"> |
48 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> | 48 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> |
49 </when> | 49 </when> |
50 </conditional> | 50 </conditional> |
51 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> | 51 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> |
52 <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" /> | 52 <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" /> |
53 <section name="adv" title="Advanced options" expanded="False"> | 53 <section name="adv" title="Advanced options" expanded="False"> |
68 <option value="contigs" selected="true">contigs</option> | 68 <option value="contigs" selected="true">contigs</option> |
69 <option value="scaffolds">scaffolds</option> | 69 <option value="scaffolds">scaffolds</option> |
70 </param> | 70 </param> |
71 </section> | 71 </section> |
72 </inputs> | 72 </inputs> |
73 | 73 |
74 <outputs> | 74 <outputs> |
75 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" > | 75 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" > |
76 <filter>log</filter> | 76 <filter>log</filter> |
77 </data> | 77 </data> |
78 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> | 78 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> |
79 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/> | 79 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/> |
80 </outputs> | 80 </outputs> |
81 | 81 |
82 <tests> | 82 <tests> |
83 <test> <!-- Test 0: Basic test --> | 83 <test> <!-- Test 0: Basic test --> |
84 <param name="lib_type" value="paired" /> | 84 <param name="lib_type" value="paired" /> |
85 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> | 85 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> |
86 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> | 86 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> |
120 </output> | 120 </output> |
121 <output name="shovill_std_log" ftype="txt" > | 121 <output name="shovill_std_log" ftype="txt" > |
122 <assert_contents> | 122 <assert_contents> |
123 <has_text text="Running: seqtk"/> | 123 <has_text text="Running: seqtk"/> |
124 <has_text text="Running: kmc"/> | 124 <has_text text="Running: kmc"/> |
125 <has_text text="Running: trimmomatic"/> | 125 <has_text_matching expression="Running:\s+\S+\s+trimmomatic"/> |
126 <has_text text="Running: lighter"/> | 126 <has_text text="Running: lighter"/> |
127 <has_text text="Running: flash"/> | 127 <has_text text="Running: flash"/> |
128 <has_text text="Running: spades"/> | 128 <has_text text="Running: spades"/> |
129 <has_text text="Running: bwa index"/> | 129 <has_text text="Running: bwa index"/> |
130 <has_text text="Running: (bwa mem"/> | 130 <has_text text="Running: (bwa mem"/> |
140 | 140 |
141 Details and options: | 141 Details and options: |
142 - Takes paired end Illumina fastq reads | 142 - Takes paired end Illumina fastq reads |
143 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF) | 143 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF) |
144 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output | 144 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output |
145 | 145 |
146 Advanced options: | 146 Advanced options: |
147 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d') | 147 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d') |
148 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100) | 148 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100) |
149 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '') | 149 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '') |
150 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '') | 150 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '') |
151 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '') | 151 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '') |