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annotate diamond_makedb.xml @ 11:e8ac2b53f262 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 41ed290dd45d61eaf0dffa0cfc61202e03bc1589
author iuc
date Thu, 02 Nov 2023 11:14:39 +0000
parents 1e3323a44643
children
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1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
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2 <description>Build database from a FASTA file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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11 <command detect_errors="aggressive">
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12 <!-- DB has two files, *.dmnd and *.tx -->
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13 <![CDATA[
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14 diamond makedb
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15 --threads "\${GALAXY_SLOTS:-12}"
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16 --in '$infile'
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17 --db ./database
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64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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19 #if str($tax_cond.tax_select) == 'yes':
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20 --taxonmap '$tax_cond.taxonmap'
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21 --taxonnodes '$tax_cond.taxonnodes'
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22 --taxonnames '$tax_cond.taxonnames'
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23 #end if
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24 ]]>
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25 </command>
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26
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27 <inputs>
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28 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
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29 <conditional name="tax_cond">
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30 <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner">
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31 <option value="yes">Yes</option>
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32 <option value="no" selected="true">No</option>
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33 </param>
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34 <when value="yes">
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1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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35 <param argument="--taxonmap" type="data" format="tabular"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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36 label="Protein accession to taxid mapping file"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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37 help="Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features.
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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38 A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored" />
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39 <param argument="--taxonnodes" type="data" format="tabular" label="Taxonomy nodes.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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40 <param argument="--taxonnames" type="data" format="tabular" label="Taxonomy names.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
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41 </when>
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42 <when value="no"/>
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43 </conditional>
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44 </inputs>
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45
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46 <outputs>
1
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47 <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <param name="infile" value="db.fasta" ftype="fasta"/>
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53 <output name="outfile" value="db.dmnd" compare="sim_size" delta="2"/>
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54 </test>
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55 <test>
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56 <param name="infile" value="db.fasta" ftype="fasta"/>
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57 <conditional name="tax_cond">
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58 <param name="tax_select" value="yes"/>
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59 <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" />
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60 <param name="taxonnodes" ftype="tabular" value="nodes.dmp" />
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61 <param name="taxonnames" ftype="tabular" value="names.dmp" />
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62 </conditional>
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63 <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/>
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64 </test>
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65 </tests>
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66
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67 <help>
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68 <![CDATA[
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69
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70 .. class:: infomark
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71
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72 **What it does**
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73
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74 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
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75 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
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76 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND is about 2,500
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77 times faster than BLASTX, finding more than 94% of all matches.
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78
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79 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
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80
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81
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82 - taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
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83
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84 - taxonnames: Path to the names.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
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85
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86 - taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
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87 ]]>
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88 </help>
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90 <expand macro="citations" />
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91 </tool>