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annotate tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml @ 0:432ea9614cc9 draft

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Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
author peterjc
date Fri, 30 Jan 2015 08:27:28 -0500
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children e98f6bd363ba
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432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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1 <tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.02">
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2 <description>low-complexity regions in protein sequences</description>
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3 <macros>
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4 <token name="@BINARY@">segmasker</token>
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5 <import>ncbi_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 ## The command is a Cheetah template which allows some Python based syntax.
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10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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11 segmasker
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12 #if $db_opts.db_opts_selector == "db":
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13 -in "${db_opts.database.fields.path}" -infmt blastdb
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14 #elif $db_opts.db_opts_selector == "histdb":
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15 -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
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16 #else:
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17 -in "$subject" -infmt fasta
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18 #end if
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19 -out "$outfile"
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20 -window $window
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21 -locut $locut
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22 -hicut $hicut
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23 -outfmt $outformat
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24 </command>
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25 <expand macro="stdio" />
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26 <inputs>
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27 <expand macro="input_conditional_protein_db" />
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28 <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" />
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29 <param name="locut" type="float" value="2.2" label="SEG low cutoff" help="(-locut)" />
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30 <param name="hicut" type="float" value="2.5" label="SEG high cutoff" help="(-hicut)" />
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31 <param name="outformat" type="select" label="Output format">
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32 <!-- seqloc_* formats are not very useful
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33 and what BLAST+ calls 'interval' is not what Galaxy calls interval format
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34 -->
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35 <option value="fasta">FASTA</option>
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36 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>
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37 <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option>
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38 <option value="maskinfo_xml">maskinfo_xml</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="outfile" format="maskinfo-asn1" label="SEG Masked File">
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43 <change_format>
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44 <when input="outformat" value="fasta" format="fasta" />
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45 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" />
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46 <!--
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47 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" />
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48 -->
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49 <when input="outformat" value="maskinfo_xml" format="xml" />
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50 </change_format>
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51 </data>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="db_opts_selector" value="file" />
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56 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
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57 <param name="window" value="12" />
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58 <param name="locut" value="2.2" />
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59 <param name="hicut" value="2.5" />
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60 <param name="outformat" value="fasta" />
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61 <output name="outfile" file="segmasker_four_human.fasta" />
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62 </test>
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63 <test>
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64 <param name="db_opts_selector" value="file" />
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65 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
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66 <param name="window" value="12" />
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67 <param name="locut" value="2.2" />
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68 <param name="hicut" value="2.5" />
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69 <param name="outformat" value="maskinfo_asn1_bin" />
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70 <output name="outfile" file="segmasker_four_human.maskinfo-asn1-binary" />
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71 </test>
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72 <test>
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73 <param name="db_opts_selector" value="file" />
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74 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
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75 <param name="window" value="12" />
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76 <param name="locut" value="2.2" />
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77 <param name="hicut" value="2.5" />
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78 <param name="outformat" value="maskinfo_asn1_text" />
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79 <output name="outfile" file="segmasker_four_human.maskinfo-asn1" />
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80 </test>
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81 </tests>
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82 <help>
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83 **What it does**
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84
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85 This tool identifies and masks out low complexity regions of a protein database (or proteins in FASTA format) by using the SEG_ algorithm.
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86
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87 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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88
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89 More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_.
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90
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91 .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/
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92 .. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706
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93
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94 **References**
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95
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96 If you use this Galaxy tool in work leading to a scientific publication please
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97 cite the following papers:
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98
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99 @REFERENCES@
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100 </help>
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101 <expand macro="blast_citations" />
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102 </tool>