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comparison macros.xml @ 15:72472698a2df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
author iuc
date Thu, 02 Mar 2023 10:38:54 +0000
parents 3061c8b029e5
children a3b35edea53a
comparison
equal deleted inserted replaced
14:3061c8b029e5 15:72472698a2df
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">5.2.0</token> 2 <token name="@TOOL_VERSION@">5.2.0</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">21.01</token> 4 <token name="@PROFILE@">21.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">quast</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">quast</requirement>
8 <requirement type="package" version="0.7.17">bwa</requirement> 8 <requirement type="package" version="0.7.17">bwa</requirement>
13 <xrefs> 13 <xrefs>
14 <xref type="bio.tools">quast</xref> 14 <xref type="bio.tools">quast</xref>
15 </xrefs> 15 </xrefs>
16 </xml> 16 </xml>
17 <xml name="gene_thresholds"> 17 <xml name="gene_thresholds">
18 <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/> 18 <param argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>
19 </xml> 19 </xml>
20 <xml name="citations"> 20 <xml name="citations">
21 <citations> 21 <citations>
22 <citation type="doi">10.1093/bioinformatics/bty266</citation> 22 <citation type="doi">10.1093/bioinformatics/bty266</citation>
23 <citation type="doi">10.1093/bioinformatics/btw379</citation> 23 <citation type="doi">10.1093/bioinformatics/btw379</citation>
24 <citation type="doi">10.1093/bioinformatics/btv697</citation> 24 <citation type="doi">10.1093/bioinformatics/btv697</citation>
25 <citation type="doi">10.1093/bioinformatics/btt086</citation> 25 <citation type="doi">10.1093/bioinformatics/btt086</citation>
26 </citations> 26 </citations>
27 </xml> 27 </xml>
28 <xml name="min_identity_macros" token_value=""> 28 <xml name="min_identity_macros" token_value="">
29 <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments 29 <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
30 with IDY% less than 80.0% will be filtered regardless of this threshold. "/> 30 </xml>
31 <xml name="custom">
32 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
33 <option value="true">Yes, specify custom names</option>
34 <option value="false" selected="true">No, use dataset names</option>
35 </param>
36 </xml>
37 <xml name="labelled_input">
38 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
39 <param argument="--labels" type="text" value="" label="Name"/>
40 </xml>
41 <xml name="reads_option">
42 <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.">
43 <option value="disabled">Disabled</option>
44 <option value="single">Illumina single-end reads</option>
45 <option value="paired">Illumina paired-end reads</option>
46 <option value="paired_collection">Illumina paired-end reads in paired collection</option>
47 <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
48 <option value="mate_paired">Illumina mate-pair reads</option>
49 <option value="pacbio">Pacbio SMRT reads</option>
50 <option value="nanopore">Nanopore reads</option>
51 </param>
31 </xml> 52 </xml>
32 </macros> 53 </macros>