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comparison shovill.xml @ 9:ee17a294d3a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0c2ed111d1186acce23eead97cf255c9af4efad1
author iuc
date Thu, 12 Oct 2023 06:59:42 +0000
parents ad80238462c1
children
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8:ad80238462c1 9:ee17a294d3a3
1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Faster SPAdes assembly of Illumina reads</description> 2 <description>Faster SPAdes assembly of Illumina reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.1.0</token> 4 <token name="@TOOL_VERSION@">1.1.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">shovill</xref> 8 <xref type="bio.tools">shovill</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
76 <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"> 76 <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">
77 <option value="paired" selected="true">Paired End</option> 77 <option value="paired" selected="true">Paired End</option>
78 <option value="collection">Paired Collection</option> 78 <option value="collection">Paired Collection</option>
79 </param> 79 </param>
80 <when value="paired"> 80 <when value="paired">
81 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> 81 <param name="R1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
82 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> 82 <param name="R2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
83 </when> 83 </when>
84 <when value="collection"> 84 <when value="collection">
85 <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"/> 85 <param name="input1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
86 </when> 86 </when>
87 </conditional> 87 </conditional>
88 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> 88 <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
89 <param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades"> 89 <param argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades">
90 <option value="skesa">skesa</option> 90 <option value="skesa">skesa</option>
91 <option value="megahit">megahit</option> 91 <option value="megahit">megahit</option>
92 <option value="velvet">velvet</option> 92 <option value="velvet">velvet</option>
93 <option value="spades" selected="true">Spades</option> 93 <option value="spades" selected="true">Spades</option>
94 </param> 94 </param>
95 <section name="adv" title="Advanced options" expanded="False"> 95 <section name="adv" title="Advanced options" expanded="False">
96 <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')" > 96 <param argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
97 <sanitizer> 97 <sanitizer>
98 <valid initial="string.printable"> 98 <valid initial="string.printable">
99 <remove value="&apos;" /> 99 <remove value="&apos;" />
100 </valid> 100 </valid>
101 <mapping initial="none"> 101 <mapping initial="none">
102 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" /> 102 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
103 </mapping> 103 </mapping>
104 </sanitizer> 104 </sanitizer>
105 </param> 105 </param>
106 <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" /> 106 <param argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
107 <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" /> 107 <param argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
108 <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" /> 108 <param argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />
109 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" /> 109 <param argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
110 <conditional name="keep_files"> 110 <conditional name="keep_files">
111 <param name="nocorr" argument="--nocorr" type="select" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)"> 111 <param argument="--nocorr" type="select" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)">
112 <option value="no_correction" selected="true">No corrections</option> 112 <option value="no_correction" selected="true">No corrections</option>
113 <option value="yes_correction">Post assembly corrections</option> 113 <option value="yes_correction">Post assembly corrections</option>
114 </param> 114 </param>
115 <when value="no_correction"/> 115 <when value="no_correction"/>
116 <when value="yes_correction"> 116 <when value="yes_correction">
117 <param name="keepfiles" argument="--keepfiles" type="boolean" truevalue="--keepfiles" checked="False" falsevalue="" label="Keep bam files" help="Keep bam files only if post-assembly correction is enable"/> 117 <param argument="--keepfiles" type="boolean" truevalue="--keepfiles" checked="False" falsevalue="" label="Keep bam files" help="Keep bam files only if post-assembly correction is enable"/>
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 <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)" /> 120 <param argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" />
121 <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)" /> 121 <param argument="--mincov" type="integer" value="2" label="Minimum contig coverage" help="Minimum coverage to call part of a contig. 0 is AUTO (default: 2)" />
122 </section> 122 </section>
123 <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" /> 123 <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" />
124 124
125 </inputs> 125 </inputs>
126 <outputs> 126 <outputs>