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

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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="BlibBuild" name="BlibBuild" version="@VERSION@.0">
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2 <description>create a library of peptide MS/MS 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 ## Need to symlink to data using name with extension that recognizes
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9 #import re
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10 #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'}
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11 #for $pl in $peak_lists:
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12 #set $dt = $pl.extension
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13 #set $bn = $pl.display_name.split('/')[-1]
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14 #set $ext = $exts[$dt.lower()]
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15 #set $input_name = $re.sub(str(r'(?i)[.]' + $dt),str('.' + $ext), str($bn))
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16 ln -s -f '${pl}' '${input_name}' &&
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17 #set $encoded_id = $__app__.security.encode_id($pl.id)
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18 echo "Spectrum:${pl.display_name}(API:${encoded_id}) " &&
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19 #end for
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20 #set $ext = $identification.extension
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21 #set $ident = $identification.display_name.split('/')[-1].replace('.' + str($identification.extension), "") + "." + $ext
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22 ln -s -f '$identification' '$ident' &&
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23 #if $existing_blib:
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24 cp '$existing_blib' spectra.blib &&
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25 #end if
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26 BlibBuild
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27 #if str($cutoff):
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28 -c $cutoff
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29 #end if
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30 #if $authority:
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31 -a $authority
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32 #end if
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33 #if $library_id:
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34 -i $library_id
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35 #end if
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36 '$ident' spectra.blib
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37 && cp spectra.blib $blib
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38 #if $convert_to_ms2:
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39 && BlibToMs2 -f '$ms2' spectra.blib
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40 #end if
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41 ]]></command>
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42 <inputs>
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43 <param name="identification" type="data" format="mzid" label="Peptide Identification Results" >
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44 <help>
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45 </help>
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46 </param>
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47 <param name="peak_lists" type="data" format="mzml,mzxml,mgf" multiple="true" optional="true"
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48 label="Spectrum Datasets used in the peptide identification"/>
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49 <param name="existing_blib" type="data" format="sqlite" label="Add to existing Blib" optional="true"/>
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50 <param name="cutoff" type="float" value="" min="0.0" max="1.0" optional="true"
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51 label="Specify the cutoff score (0-1)"
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52 help=" below which peptide-spectrum matches will be excluded from the library."/>
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53 <param name="authority" type="text" value="" optional="true" label="LSID authority. Default proteome.gs.washington.edu"/>
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54 <param name="library_id" type="text" value="" optional="true" label="LSID library ID. Default uses file name"/>
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55 <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/>
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56 </inputs>
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57 <outputs>
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58 <data name="blib" format="sqlite" label="Blib from ${on_string}" from_work_dir="spectra.blib" />
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59 <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" >
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60 <filter>convert_to_ms2 == True</filter>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="identification" ftype="mzid" value="msgf-test.mzid"/>
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66 <param name="peak_lists" ftype="mzml" value="msgf-test.mzML"/>
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67 <param name="convert_to_ms2" value="True"/>
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68 <output name="ms2">
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69 <assert_contents>
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70 <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
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71 <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
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72 </assert_contents>
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73 </output>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
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78
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79 BlibBuild_ creates a library of peptide MS/MS spectra from a variety of different database search results.
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80
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81 ::
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82
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83 Usage: BlibBuild [options] <*.blib|*.pep.xml|*.pep.XML|*.pepXML|*.sqt|*.perc.xml|*.dat|*.xtan.xml|*.idpXML|*.group.xml|*.pride.xml|*.msf|*.pdResult|*.mzid|*msms.txt|*final_fragment.csv|*.proxl.xml|*.ssl|*.mlb|*.tsv|*.osw>+ <library_name>
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84 -o Overwrite existing library. Default append.
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85 -S <filename> Read from file as though it were stdin.
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86 -s Result file names from stdin. e.g. ls *sqt | BlibBuild -s new.blib.
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87 -u Ignore peptides except those with the unmodified sequences from stdin.
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88 -U Ignore peptides except those with the modified sequences from stdin.
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89 -H Use more than one decimal place when describing mass modifications.
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90 -C <file size> Minimum file size required to use caching for .dat files. Specifiy units as B,K,G or M. Default 800M.
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91 -c <cutoff> Score threshold (0-1) for PSMs to be included in library. Higher threshold is more exclusive.
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92 -v <level> Level of output to stderr (silent, error, status, warn). Default status.
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93 -L Write status and warning messages to log file.
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94 -m <size> SQLite memory cache size in Megs. Default 250M.
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95 -l <level> ZLib compression level (0-?). Default 3.
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96 -i <library_id> LSID library ID. Default uses file name.
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97 -a <authority> LSID authority. Default proteome.gs.washington.edu.
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98 -x <filename> Specify the path of XML modifications file for parsing MaxQuant files.
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99 -P <float> Specify pusher interval for Waters final_fragment.csv files.
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100 -d [<filename>] Document the .blib format by writing SQLite commands to a file, or stdout if no filename is given.
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101
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102
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103 .. _BlibBuild: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild
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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>