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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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-1:000000000000 0:5a4801b7d106
1 <tool id="BlibSearch" name="BlibSearch" version="@VERSION@.0">
2 <description>search a spectrum library for matches to query spectra</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'}
9 #set $ext = $exts[$spectrum_file.extension.lower()]
10 #set $spectrum_name = $spectrum_file.display_name.split('/')[-1].replace($spectrum_file.extension, "") + "." + $ext
11 ln -s -f '${spectrum_file}' '${spectrum_name}' &&
12 #set $blib_name = $blib.display_name.split('/')[-1].replace($blib.extension, "") + ".blib"
13 ln -s -f '$blib' '$blib_name' &&
14 BlibSearch
15 --clear-precursor $clear_precursor
16 --topPeaksForSearch $topPeaksForSearch
17 --mz-window $mz_window
18 --min-peaks $min_peaks
19 --low-charge $low_charge
20 --high-charge $high_charge
21 --report-matches $report_matches
22 $preserve_order
23 ## --psm-result-file '$psms'
24 --report-file temp.report
25 '$spectrum_name' '$blib_name'
26 && grep -v '^$' temp.report > '$report'
27 ]]></command>
28 <inputs>
29 <param name="spectrum_file" type="data" format="mzml,mzxml,mgf,ms2" label="Spectrum file to search"/>
30 <param name="blib" type="data" format="sqlite" label="Filtered Blib"/>
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."/>
32 <param name="topPeaksForSearch" type="integer" value="100" label="Use ARG of the highest intensity peaks."/>
33 <param name="mz_window" type="float" value="3" label="Compare query to library spectra with precursor m/z +/- ARG."/>
34 <param name="min_peaks" type="integer" value="20" label="Search only spectra with charge no less than ARG."/>
35 <param name="low_charge" type="integer" value="1" label="Search only spectra with charge no less than ARG."/>
36 <param name="high_charge" type="integer" value="5" label="Search only spectra with charge no higher than ARG."/>
37 <param name="report_matches" type="integer" value="5" label="Return ARG of the best matches for each query. Use -1 to report all."/>
38 <param name="preserve_order" type="boolean" truevalue="--preserve-order" falsevalue="" checked="false"
39 label="Search spectra in the order they appear in the file."
40 help="Default to search as sorted by precursor m/z."/>
41 </inputs>
42 <outputs>
43 <data name="report" format="tabular" label="${spectrum_file.name}.report">
44 <actions>
45 <action name="comment_lines" type="metadata" default="13" />
46 <action name="column_names" type="metadata" default="Query,LibId,LibSpec,rank,dotp,query-mz,query-z,lib-mz,lib-z,copies,candidates,sequence,TIC-raw,bp-mz-raw,bp-raw,lbp-mz-raw,num-peaks,matched-ions" />
47 </actions>
48 </data>
49 <!--
50 <data name="psms" format="tabular" label="${spectrum_file.name}.psms"/>
51 -->
52 </outputs>
53 <tests>
54 <test>
55 <param name="spectrum_file" ftype="mzml" value="msgf-test.mzML"/>
56 <param name="blib" ftype="sqlite" value="msgf_filterd.blib"/>
57 <output name="report">
58 <assert_contents>
59 <has_text text="LibSpec" />
60 <has_text text="VIYTTNAVEAVHRQFRKLTK" />
61 </assert_contents>
62 </output>
63 </test>
64 </tests>
65 <help><![CDATA[
66 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
67
68 BlibSearch_ creates a library of peptide MS/MS spectra from a variety of different database search results.
69
70 ::
71
72 Usage: BlibSearch [options] <spectrum-file> <library>[+]
73
74 Options:
75 -c [ --clear-precursor ] arg (=1) Remove the peaks in a X m/z window around
76 the precursor from the query and library
77 spectrum.
78 --topPeaksForSearch arg (=100) Use ARG of the highest intensity peaks.
79 -w [ --mz-window ] arg (=3) Compare query to library spectra with
80 precursor m/z +/- ARG.
81 -n [ --min-peaks ] arg (=20) Search only spectra with charge no less
82 than ARG.
83 -L [ --low-charge ] arg (=1) Search only spectra with charge no less
84 than ARG.
85 -H [ --high-charge ] arg (=5) Search only spectra with charge no higher
86 than ARG.
87 -m [ --report-matches ] arg (=5) Return ARG of the best matches for each
88 query. Use -1 to report all.
89 --psm-result-file arg Return results in a .psm file named ARG.
90 -R [ --report-file ] arg Return results in report file named ARG.
91 Default is <spectrum file name>.report.
92 --preserve-order Search spectra in the order they appear in
93 the file. Default to search as sorted by
94 precursor m/z.
95 -p [ --parameter-file ] arg File containing search parameters.
96 Command line values override file values.
97 -v [ --verbosity ] arg (=status) Control the level of output to stderr.
98 (silent, error, status, warn, debug,
99 detail, all) Default status.
100 -h [ --help ] Print help message.
101
102
103 .. _BlibSearch: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibSearch
104 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
105 ]]></help>
106 <expand macro="citations" />
107 </tool>
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