Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
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date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 3034ce97dd33 |
children | 31e517610e1f |
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1 <tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="@WRAPPER_VERSION@"> |
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2 <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> |
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3 <description>masks low complexity regions</description> |
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4 <macros> |
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5 <token name="@BINARY@">dustmasker</token> |
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6 <import>ncbi_macros.xml</import> |
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7 </macros> |
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8 <expand macro="preamble" /> |
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9 <command detect_errors="aggressive"> |
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10 ## The command is a Cheetah template which allows some Python based syntax. |
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11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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12 dustmasker |
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13 #if $db_opts.db_opts_selector == "db": |
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14 -in '${db_opts.database.fields.path}' -infmt blastdb |
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15 #elif $db_opts.db_opts_selector == "histdb": |
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16 -in '${os.path.join($db_opts.histdb.files_path, "blastdb")}' -infmt blastdb |
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17 #else: |
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18 -in '$subject' -infmt fasta |
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19 #end if |
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20 -out '$outfile' |
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21 -window $window -level $level -linker $linker -outfmt $outformat |
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22 </command> |
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23 <inputs> |
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24 <expand macro="input_conditional_nucleotide_db" /> |
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25 <param argument="-window" type="integer" value="64" label="DUST window length" /> |
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26 <param argument="-level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> |
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27 <param argument="-linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> |
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28 <param name="outformat" argument="-outfmt" type="select" label="Output format"> |
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29 <!-- seqloc_* formats are not very useful |
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30 and what BLAST+ calls 'interval' is not what Galaxy calls interval format |
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31 --> |
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32 <option value="fasta">FASTA</option> |
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33 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> |
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34 <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option> |
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35 <option value="maskinfo_xml">maskinfo_xml</option> |
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36 </param> |
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37 </inputs> |
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38 <outputs> |
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39 <data name="outfile" format="maskinfo-asn1" label="DUST Masked File"> |
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40 <change_format> |
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41 <when input="outformat" value="fasta" format="fasta" /> |
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42 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> |
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43 <!-- |
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44 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> |
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45 --> |
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46 <when input="outformat" value="maskinfo_xml" format="xml" /> |
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47 </change_format> |
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48 </data> |
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49 </outputs> |
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50 <tests> |
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51 <test> |
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52 <param name="db_opts_selector" value="file" /> |
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53 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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54 <param name="window" value="64" /> |
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55 <param name="level" value="20" /> |
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56 <param name="linker" value="1" /> |
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57 <param name="outformat" value="fasta" /> |
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58 <output name="outfile" file="dustmasker_three_human.fasta" /> |
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59 </test> |
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60 <test> |
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61 <param name="db_opts_selector" value="file" /> |
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62 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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63 <param name="window" value="64" /> |
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64 <param name="level" value="20" /> |
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65 <param name="linker" value="1" /> |
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66 <param name="outformat" value="maskinfo_asn1_bin" /> |
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67 <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> |
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68 </test> |
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69 <test> |
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70 <param name="db_opts_selector" value="file" /> |
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71 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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72 <param name="window" value="64" /> |
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73 <param name="level" value="20" /> |
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74 <param name="linker" value="1" /> |
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75 <param name="outformat" value="maskinfo_asn1_text" /> |
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76 <output name="outfile" file="dustmasker_three_human.maskinfo-asn1" /> |
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77 </test> |
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78 </tests> |
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79 <help> |
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80 **What it does** |
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81 |
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82 This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST_ algorithm. |
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83 |
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84 If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. |
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85 |
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86 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. |
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87 |
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88 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
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89 .. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 |
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90 |
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91 **References** |
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92 |
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93 If you use this Galaxy tool in work leading to a scientific publication please |
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94 cite the following papers: |
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95 |
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96 @REFERENCES@ |
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97 </help> |
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98 <expand macro="blast_citations" /> |
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99 </tool> |