Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_makeprofiledb.xml @ 26:2889433c7ae1 draft
v0.3.3 - fixed legacy dependecy definition
author | peterjc |
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date | Sat, 20 Jul 2019 18:36:36 -0400 |
parents | e25d3acf6e68 |
children | 6f8ea4b9a2c4 |
rev | line source |
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1 <tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@"> |
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2 <description>Make profile database</description> |
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3 <macros> |
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4 <token name="@BINARY@">makeprofiledb</token> |
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5 <import>ncbi_macros.xml</import> |
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6 </macros> |
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7 <expand macro="preamble" /> |
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8 <command detect_errors="aggressive" strict="true"> |
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9 ##Unlike makeblastdb, makeprofiledb needs directory to exist already: |
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10 mkdir -p $outfile.files_path && |
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11 makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}' |
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12 |
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13 ##We turn $input_file into $infiles with a configfile entry defined below |
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14 -in '$infiles' |
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15 |
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16 #if $title: |
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17 -title '$title' |
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18 #else: |
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19 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful |
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20 -title 'Profile Database' |
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21 #end if |
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22 |
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23 -threshold $threshold |
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24 |
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25 #if str($contain_pssm_scores.contain_pssm_scores_type) == 'no': |
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26 -gapopen $contain_pssm_scores.gapopen |
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27 -gapextend $contain_pssm_scores.gapextend |
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28 -scale $contain_pssm_scores.scale |
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Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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29 -matrix $contain_pssm_scores.matrix |
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30 #end if |
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31 |
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32 -obsr_threshold $obsr_threshold |
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33 -exclude_invalid $exclude_invalid |
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34 |
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35 -logfile '$outfile' |
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36 </command> |
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37 <configfiles> |
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38 <configfile name="infiles"> |
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39 #for $infile in $input_file |
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40 ${infile} |
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41 #end for |
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42 </configfile> |
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43 </configfiles> |
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44 <inputs> |
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45 <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="pssm-asn1" |
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46 label="Input PSSM files(s)" |
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47 help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" /> |
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48 |
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49 <param argument="-title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" /> |
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50 <param argument="-threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" /> |
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51 |
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52 <!-- output options --> |
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53 <!-- Initially we're only offering the default, RPS databases for use with rpsblast and rpstblastn |
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54 <param name="dbtype" type="select" display="radio" label="Type of database"> |
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55 <option value="cobalt">Cobalt</option> |
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56 <option value="delta">Delta</option> |
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57 <option value="rps" selected="true">RPS</option> |
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58 </param> |
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59 --> |
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60 |
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61 <conditional name="contain_pssm_scores"> |
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62 <param name="contain_pssm_scores_type" type="select" label="Does your input file contain PSSM scores?"> |
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63 <option value="yes" selected="true">Yes</option> |
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64 <option value="no">No</option> |
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65 </param> |
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66 <when value="yes" /> |
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67 <when value="no"> |
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68 <param argument="-gapopen" type="integer" size="5" value="" label="Cost to open a gap" /> |
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69 <param argument="-gapextend" type="integer" size="5" value="" label="Cost to extend a gap" /> |
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70 <param argument="-scale" type="float" size="5" value="" label="PSSM scale factor" /> |
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71 <expand macro="input_scoring_matrix" /> |
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72 </when> |
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73 </conditional> |
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74 |
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75 <!-- Delta Blast Options --> |
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76 <param argument="-exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true" |
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77 label="Exclude invalid domains?" |
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78 help="Exclude domains that do not pass validation test" /> |
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79 <param argument="-obsr_threshold" type="float" size="5" value="6.0" |
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80 label="Observation threshold" |
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81 help="Exclude domains with with maximum number of independent observations below this threshold" /> |
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82 </inputs> |
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83 <outputs> |
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84 <data name="outfile" format="blastdbd" label="RPS database from ${on_string}" /> |
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Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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85 </outputs> |
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86 <tests> |
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87 <test> |
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88 <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" /> |
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89 <param name="title" value="Just 2 PSSM matrices" /> |
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90 <param name="contain_pssm_scores_type" value="yes" /> |
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91 <output name="outfile" file="empty_file.dat" ftype="blastdbd" > |
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92 <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" /> |
26 | 93 <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" compare="sim_size" delta="8" /> |
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94 <extra_files type="file" value="cd00003_and_cd00008.psq" name="blastdb.psq" /> |
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95 <extra_files type="file" value="cd00003_and_cd00008.freq" name="blastdb.freq" /> |
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96 <extra_files type="file" value="cd00003_and_cd00008.loo" name="blastdb.loo" /> |
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97 <extra_files type="file" value="cd00003_and_cd00008.psd" name="blastdb.psd" /> |
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98 <extra_files type="file" value="cd00003_and_cd00008.psi" name="blastdb.psi" /> |
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99 <extra_files type="file" value="cd00003_and_cd00008.rps" name="blastdb.rps" /> |
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100 <extra_files type="file" value="cd00003_and_cd00008.aux" name="blastdb.aux" /> |
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101 </output> |
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102 </test> |
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103 </tests> |
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104 <help> |
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105 **What it does** |
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106 |
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107 Make a protein domain profile database (for use with RPS-BLAST or RSP-TBLASTN) |
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108 from one or more Position Specific Scoring Matrices (PSSM) files in the NCBI |
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109 "scoremat" ASN.1 format (usually named ``*.smp``). |
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110 |
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111 This is a wrapper for the NCBI BLAST+ tool 'makeprofiledb'. |
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112 |
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113 More information about makeprofiledb can be found in the `BLAST Command Line Applications User Manual`_. |
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114 |
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115 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
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116 |
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117 |
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118 **References** |
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119 |
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120 If you use this Galaxy tool in work leading to a scientific publication please |
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121 cite the following papers: |
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122 |
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Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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123 @REFERENCES@ |
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124 </help> |
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125 <expand macro="blast_citations" /> |
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Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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126 </tool> |