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comparison BlibToMs2.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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-1:000000000000 0:5a4801b7d106
1 <tool id="BlibToMs2" name="BlibToMs2" version="@VERSION@.0">
2 <description>convert spectrum library blib to MS2 format</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 BlibToMs2
9 --mz-precision $mz_precision
10 --intensity-precision $intensity_precision
11 --mod-precision $mod_precision
12 -f '$output'
13 '$blib'
14 ]]></command>
15 <inputs>
16 <param name="blib" type="data" format="sqlite" label="Blib to convert to MS2"/>
17 <param name="mz_precision" type="integer" value="2" min="1" max="6"
18 label="Precision for peak m/z printed to ms2"
19 help="--mz-precision"/>
20 <param name="intensity_precision" type="integer" value="1" min="1" max="6"
21 label="Precision for peak intensities printed to ms2"
22 help="--intensity-precision"/>
23 <param name="mod_precision" type="integer" value="1" min="1" max="6"
24 label="Precision for modification masses"
25 help="--mod-precision"/>
26 </inputs>
27 <outputs>
28 <data name="output" format="ms2" label="${blib.name.rsplit('.',1)[0]}.ms2"/>
29 </outputs>
30 <tests>
31 <test>
32 <param name="blib" ftype="sqlite" value="msgf_filterd.blib"/>
33 <output name="output">
34 <assert_contents>
35 <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
36 <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
37 </assert_contents>
38 </output>
39 </test>
40 </tests>
41 <help><![CDATA[
42 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
43
44 BlibToMs2_ creates a library of peptide MS/MS spectra from a variety of different database search results.
45
46 ::
47
48 Usage: BlibToMs2 [options] <library>
49
50 Options:
51 -f [ --file-name ] arg Name the output ms2 file. Default is
52 <library name>.ms2.
53 -m [ --mz-precision ] arg (=2) Precision for peak m/z printed to ms2.
54 Default 2.
55 -i [ --intensity-precision ] arg (=1) Precision for peak intensities.
56 Default 1.
57 -p [ --mod-precision ] arg (=-1) Precision for modification masses.
58 Default -1 (use value in PeptideModSeq
59 column).
60 -p [ --parameter-file ] arg File containing search parameters.
61 Command line values override file
62 values.
63 -v [ --verbosity ] arg (=status) Control the level of output to stderr.
64 (silent, error, status, warn, debug,
65 detail, all) Default status.
66 -h [ --help ] Print help message.
67
68
69 .. _BlibToMs2: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibToMs2
70 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
71 ]]></help>
72 <expand macro="citations" />
73 </tool>