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annotate BlibSearch.xml @ 0:5a4801b7d106 draft default tip

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author galaxyp
date Tue, 08 May 2018 14:16:45 -0400
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5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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1 <tool id="BlibSearch" name="BlibSearch" version="@VERSION@.0">
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2 <description>search a spectrum library for matches to query spectra</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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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'}
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9 #set $ext = $exts[$spectrum_file.extension.lower()]
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10 #set $spectrum_name = $spectrum_file.display_name.split('/')[-1].replace($spectrum_file.extension, "") + "." + $ext
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11 ln -s -f '${spectrum_file}' '${spectrum_name}' &&
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12 #set $blib_name = $blib.display_name.split('/')[-1].replace($blib.extension, "") + ".blib"
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13 ln -s -f '$blib' '$blib_name' &&
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14 BlibSearch
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15 --clear-precursor $clear_precursor
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16 --topPeaksForSearch $topPeaksForSearch
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17 --mz-window $mz_window
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18 --min-peaks $min_peaks
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19 --low-charge $low_charge
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20 --high-charge $high_charge
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21 --report-matches $report_matches
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22 $preserve_order
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23 ## --psm-result-file '$psms'
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24 --report-file temp.report
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25 '$spectrum_name' '$blib_name'
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26 && grep -v '^$' temp.report > '$report'
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27 ]]></command>
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28 <inputs>
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29 <param name="spectrum_file" type="data" format="mzml,mzxml,mgf,ms2" label="Spectrum file to search"/>
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30 <param name="blib" type="data" format="sqlite" label="Filtered Blib"/>
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31 <param name="clear_precursor" type="boolean" value="true" label="Remove the peaks in a X m/z window around the precursor from the query and library spectrum."/>
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32 <param name="topPeaksForSearch" type="integer" value="100" label="Use ARG of the highest intensity peaks."/>
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33 <param name="mz_window" type="float" value="3" label="Compare query to library spectra with precursor m/z +/- ARG."/>
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34 <param name="min_peaks" type="integer" value="20" label="Search only spectra with charge no less than ARG."/>
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35 <param name="low_charge" type="integer" value="1" label="Search only spectra with charge no less than ARG."/>
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36 <param name="high_charge" type="integer" value="5" label="Search only spectra with charge no higher than ARG."/>
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37 <param name="report_matches" type="integer" value="5" label="Return ARG of the best matches for each query. Use -1 to report all."/>
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38 <param name="preserve_order" type="boolean" truevalue="--preserve-order" falsevalue="" checked="false"
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39 label="Search spectra in the order they appear in the file."
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40 help="Default to search as sorted by precursor m/z."/>
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41 </inputs>
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42 <outputs>
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43 <data name="report" format="tabular" label="${spectrum_file.name}.report">
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44 <actions>
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45 <action name="comment_lines" type="metadata" default="13" />
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46 <action name="column_names" type="metadata" default="Query,LibId,LibSpec,rank,dotp,query-mz,query-z,lib-mz,lib-z,copies,candidates,sequence,TIC-raw,bp-mz-raw,bp-raw,lbp-mz-raw,num-peaks,matched-ions" />
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47 </actions>
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48 </data>
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49 <!--
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50 <data name="psms" format="tabular" label="${spectrum_file.name}.psms"/>
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51 -->
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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="spectrum_file" ftype="mzml" value="msgf-test.mzML"/>
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56 <param name="blib" ftype="sqlite" value="msgf_filterd.blib"/>
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57 <output name="report">
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58 <assert_contents>
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59 <has_text text="LibSpec" />
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60 <has_text text="VIYTTNAVEAVHRQFRKLTK" />
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61 </assert_contents>
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62 </output>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
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67
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68 BlibSearch_ creates a library of peptide MS/MS spectra from a variety of different database search results.
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69
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70 ::
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71
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72 Usage: BlibSearch [options] <spectrum-file> <library>[+]
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73
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74 Options:
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75 -c [ --clear-precursor ] arg (=1) Remove the peaks in a X m/z window around
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76 the precursor from the query and library
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77 spectrum.
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78 --topPeaksForSearch arg (=100) Use ARG of the highest intensity peaks.
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79 -w [ --mz-window ] arg (=3) Compare query to library spectra with
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80 precursor m/z +/- ARG.
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81 -n [ --min-peaks ] arg (=20) Search only spectra with charge no less
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82 than ARG.
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83 -L [ --low-charge ] arg (=1) Search only spectra with charge no less
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84 than ARG.
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85 -H [ --high-charge ] arg (=5) Search only spectra with charge no higher
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86 than ARG.
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87 -m [ --report-matches ] arg (=5) Return ARG of the best matches for each
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88 query. Use -1 to report all.
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89 --psm-result-file arg Return results in a .psm file named ARG.
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90 -R [ --report-file ] arg Return results in report file named ARG.
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91 Default is <spectrum file name>.report.
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92 --preserve-order Search spectra in the order they appear in
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93 the file. Default to search as sorted by
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94 precursor m/z.
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95 -p [ --parameter-file ] arg File containing search parameters.
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96 Command line values override file values.
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97 -v [ --verbosity ] arg (=status) Control the level of output to stderr.
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98 (silent, error, status, warn, debug,
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99 detail, all) Default status.
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100 -h [ --help ] Print help message.
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101
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102
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103 .. _BlibSearch: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibSearch
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104 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
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105 ]]></help>
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106 <expand macro="citations" />
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107 </tool>
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108
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109
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110