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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
author iuc
date Tue, 12 Nov 2024 12:46:19 +0000
parents 72472698a2df
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <macros>
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2 <token name="@TOOL_VERSION@">5.3.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">23.02</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">quast</requirement>
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8 <requirement type="package" version="0.7.18">bwa</requirement>
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9 <requirement type="package" version="2.31.1">bedtools</requirement>
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10 <requirement type="package" version="2.76">perl-gd</requirement>
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11 </requirements>
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12 </xml>
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13 <xml name="bio_tools">
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14 <xrefs>
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15 <xref type="bio.tools">quast</xref>
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16 </xrefs>
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17 </xml>
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18 <xml name="gene_thresholds">
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19 <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"/>
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20 </xml>
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21 <xml name="citations">
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22 <citations>
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23 <citation type="doi">10.1093/bioinformatics/bty266</citation>
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24 <citation type="doi">10.1093/bioinformatics/btw379</citation>
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25 <citation type="doi">10.1093/bioinformatics/btv697</citation>
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26 <citation type="doi">10.1093/bioinformatics/btt086</citation>
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27 </citations>
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28 </xml>
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29 <xml name="min_identity_macros" token_value="">
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30 <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. "/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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31 </xml>
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32 <xml name="custom">
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33 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
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34 <option value="true">Yes, specify custom names</option>
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35 <option value="false" selected="true">No, use dataset names</option>
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36 </param>
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37 </xml>
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38 <xml name="labelled_input">
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39 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
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40 <param argument="--labels" type="text" value="" label="Name"/>
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41 </xml>
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42 <xml name="reads_option">
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43 <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.">
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44 <option value="disabled">Disabled</option>
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45 <option value="single">Illumina single-end reads</option>
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46 <option value="paired">Illumina paired-end reads</option>
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47 <option value="paired_collection">Illumina paired-end reads in paired collection</option>
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48 <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
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49 <option value="mate_paired">Illumina mate-pair reads</option>
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50 <option value="pacbio">Pacbio SMRT reads</option>
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51 <option value="nanopore">Nanopore reads</option>
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52 </param>
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53 </xml>
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54 </macros>