Mercurial > repos > galaxyp > bibliospec

annotate BlibToMs2.xml @ 0:5a4801b7d106 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
1 <tool id="BlibToMs2" name="BlibToMs2" version="@VERSION@.0">
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
2 <description>convert spectrum library blib to MS2 format</description>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
3 <macros>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
4 <import>macros.xml</import>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
5 </macros>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
6 <expand macro="requirements" />
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
8 BlibToMs2
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
9 --mz-precision $mz_precision
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
10 --intensity-precision $intensity_precision
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
11 --mod-precision $mod_precision
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
12 -f '$output'
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
13 '$blib'
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
14 ]]></command>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
15 <inputs>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
16 <param name="blib" type="data" format="sqlite" label="Blib to convert to MS2"/>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
17 <param name="mz_precision" type="integer" value="2" min="1" max="6"
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
18 label="Precision for peak m/z printed to ms2"
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
19 help="--mz-precision"/>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
20 <param name="intensity_precision" type="integer" value="1" min="1" max="6"
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
21 label="Precision for peak intensities printed to ms2"
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
22 help="--intensity-precision"/>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
23 <param name="mod_precision" type="integer" value="1" min="1" max="6"
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
24 label="Precision for modification masses"
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
25 help="--mod-precision"/>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
26 </inputs>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
27 <outputs>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
28 <data name="output" format="ms2" label="${blib.name.rsplit('.',1)[0]}.ms2"/>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
29 </outputs>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
30 <tests>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
31 <test>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
32 <param name="blib" ftype="sqlite" value="msgf_filterd.blib"/>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
33 <output name="output">
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
34 <assert_contents>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
35 <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
36 <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
37 </assert_contents>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
38 </output>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
39 </test>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
40 </tests>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
41 <help><![CDATA[
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
42 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
43
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
44 BlibToMs2_ creates a library of peptide MS/MS spectra from a variety of different database search results.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
45
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
46 ::
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
47
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
48 Usage: BlibToMs2 [options] <library>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
49
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
50 Options:
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
51 -f [ --file-name ] arg Name the output ms2 file. Default is
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
52 <library name>.ms2.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
53 -m [ --mz-precision ] arg (=2) Precision for peak m/z printed to ms2.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
54 Default 2.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
55 -i [ --intensity-precision ] arg (=1) Precision for peak intensities.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
56 Default 1.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
57 -p [ --mod-precision ] arg (=-1) Precision for modification masses.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
58 Default -1 (use value in PeptideModSeq
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
59 column).
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
60 -p [ --parameter-file ] arg File containing search parameters.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
61 Command line values override file
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
62 values.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
63 -v [ --verbosity ] arg (=status) Control the level of output to stderr.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
64 (silent, error, status, warn, debug,
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
65 detail, all) Default status.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
66 -h [ --help ] Print help message.
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
67
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
68
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
69 .. _BlibToMs2: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibToMs2
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
70 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
71 ]]></help>
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
72 <expand macro="citations" />
5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
diff changeset
73 </tool>