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comparison 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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-1:000000000000 0:5a4801b7d106
1 <tool id="BlibBuild" name="BlibBuild" version="@VERSION@.0">
2 <description>create a library of peptide MS/MS spectra</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 ## Need to symlink to data using name with extension that recognizes
9 #import re
10 #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'}
11 #for $pl in $peak_lists:
12 #set $dt = $pl.extension
13 #set $bn = $pl.display_name.split('/')[-1]
14 #set $ext = $exts[$dt.lower()]
15 #set $input_name = $re.sub(str(r'(?i)[.]' + $dt),str('.' + $ext), str($bn))
16 ln -s -f '${pl}' '${input_name}' &&
17 #set $encoded_id = $__app__.security.encode_id($pl.id)
18 echo "Spectrum:${pl.display_name}(API:${encoded_id}) " &&
19 #end for
20 #set $ext = $identification.extension
21 #set $ident = $identification.display_name.split('/')[-1].replace('.' + str($identification.extension), "") + "." + $ext
22 ln -s -f '$identification' '$ident' &&
23 #if $existing_blib:
24 cp '$existing_blib' spectra.blib &&
25 #end if
26 BlibBuild
27 #if str($cutoff):
28 -c $cutoff
29 #end if
30 #if $authority:
31 -a $authority
32 #end if
33 #if $library_id:
34 -i $library_id
35 #end if
36 '$ident' spectra.blib
37 && cp spectra.blib $blib
38 #if $convert_to_ms2:
39 && BlibToMs2 -f '$ms2' spectra.blib
40 #end if
41 ]]></command>
42 <inputs>
43 <param name="identification" type="data" format="mzid" label="Peptide Identification Results" >
44 <help>
45 </help>
46 </param>
47 <param name="peak_lists" type="data" format="mzml,mzxml,mgf" multiple="true" optional="true"
48 label="Spectrum Datasets used in the peptide identification"/>
49 <param name="existing_blib" type="data" format="sqlite" label="Add to existing Blib" optional="true"/>
50 <param name="cutoff" type="float" value="" min="0.0" max="1.0" optional="true"
51 label="Specify the cutoff score (0-1)"
52 help=" below which peptide-spectrum matches will be excluded from the library."/>
53 <param name="authority" type="text" value="" optional="true" label="LSID authority. Default proteome.gs.washington.edu"/>
54 <param name="library_id" type="text" value="" optional="true" label="LSID library ID. Default uses file name"/>
55 <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/>
56 </inputs>
57 <outputs>
58 <data name="blib" format="sqlite" label="Blib from ${on_string}" from_work_dir="spectra.blib" />
59 <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" >
60 <filter>convert_to_ms2 == True</filter>
61 </data>
62 </outputs>
63 <tests>
64 <test>
65 <param name="identification" ftype="mzid" value="msgf-test.mzid"/>
66 <param name="peak_lists" ftype="mzml" value="msgf-test.mzML"/>
67 <param name="convert_to_ms2" value="True"/>
68 <output name="ms2">
69 <assert_contents>
70 <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
71 <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
72 </assert_contents>
73 </output>
74 </test>
75 </tests>
76 <help><![CDATA[
77 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
78
79 BlibBuild_ creates a library of peptide MS/MS spectra from a variety of different database search results.
80
81 ::
82
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>
84 -o Overwrite existing library. Default append.
85 -S <filename> Read from file as though it were stdin.
86 -s Result file names from stdin. e.g. ls *sqt | BlibBuild -s new.blib.
87 -u Ignore peptides except those with the unmodified sequences from stdin.
88 -U Ignore peptides except those with the modified sequences from stdin.
89 -H Use more than one decimal place when describing mass modifications.
90 -C <file size> Minimum file size required to use caching for .dat files. Specifiy units as B,K,G or M. Default 800M.
91 -c <cutoff> Score threshold (0-1) for PSMs to be included in library. Higher threshold is more exclusive.
92 -v <level> Level of output to stderr (silent, error, status, warn). Default status.
93 -L Write status and warning messages to log file.
94 -m <size> SQLite memory cache size in Megs. Default 250M.
95 -l <level> ZLib compression level (0-?). Default 3.
96 -i <library_id> LSID library ID. Default uses file name.
97 -a <authority> LSID authority. Default proteome.gs.washington.edu.
98 -x <filename> Specify the path of XML modifications file for parsing MaxQuant files.
99 -P <float> Specify pusher interval for Waters final_fragment.csv files.
100 -d [<filename>] Document the .blib format by writing SQLite commands to a file, or stdout if no filename is given.
101
102
103 .. _BlibBuild: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild
104 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
105 ]]></help>
106 <expand macro="citations" />
107 </tool>