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comparison BlibFilter.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="BlibFilter" name="BlibFilter" version="@VERSION@.0">
2 <description>remove redundant spectra from a library</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 BlibFilter
9 --min-peaks $min_peaks
10 --min-score $min_score
11 --best-scoring $best_scoring
12 '$redundant_blib' '$filtered_blib'
13 #if $convert_to_ms2:
14 && BlibToMs2 -f '$ms2' '$filtered_blib'
15 #end if
16 ]]></command>
17 <inputs>
18 <param name="redundant_blib" type="data" format="sqlite" label="Redundant Blib"/>
19 <param name="min_peaks" type="integer" value="1" min="1"
20 label="Only include spectra with at least this peaks"
21 help="--min-peaks"/>
22 <param name="min_score" type="float" value="0" min="0"
23 label="Best spectrum must have at least this average score to be included."
24 help="--min-score"/>
25 <param name="best_scoring" type="boolean" truevalue="1" falsevalue="0" checked="false"
26 label="Use best scoring"/>
27 <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/>
28 </inputs>
29 <outputs>
30 <data name="filtered_blib" format="sqlite" label="Filtered Blib"/>
31 <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" >
32 <filter>convert_to_ms2 == True</filter>
33 </data>
34 </outputs>
35 <tests>
36 <test>
37 <param name="redundant_blib" ftype="sqlite" value="msgf.blib"/>
38 <param name="convert_to_ms2" value="True"/>
39 <output name="ms2">
40 <assert_contents>
41 <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
42 <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
43 </assert_contents>
44 </output>
45 </test>
46 </tests>
47 <help><![CDATA[
48 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
49
50 BlibFilter_ creates a library of peptide MS/MS spectra from a variety of different database search results.
51
52 ::
53
54 Usage: BlibFilter [options] <redundant-library> <filtered-library>
55
56 Options:
57 -m [ --memory-cache ] arg (=250) SQLite memory cache size in Megs. Default
58 250M.
59 -n [ --min-peaks ] arg (=1) Only include spectra with at least this
60 many peaks. Default 1.
61 -s [ --min-score ] arg (=0) Best spectrum must have at least this
62 average score to be included. Default 0.
63 -b [ --best-scoring ] arg (=0) Description of option. Default false.
64 -p [ --parameter-file ] arg File containing search parameters. Command
65 line values override file values.
66 -v [ --verbosity ] arg (=status) Control the level of output to stderr.
67 (silent, error, status, warn, debug,
68 detail, all) Default status.
69 -h [ --help ] Print help message.
70
71
72 .. _BlibFilter: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibFilter
73 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
74 ]]></help>
75 <expand macro="citations" />
76 </tool>