Mercurial > repos > galaxyp > msgfplus

comparison msgfplus.xml @ 0:dbc77b37e20f draft

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/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
author galaxyp
date Fri, 06 Nov 2015 14:31:57 -0500
parents
children 08b316ae9ec4
comparison
equal deleted inserted replaced
-1:000000000000 0:dbc77b37e20f
1 <tool id="msgfplus" name="MS-GF+" version="0.1">
2 <description>
3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
4 </description>
5 <requirements>
6 <requirement type="package" version="10089">msgfplus</requirement>
7 <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" level="fatal" description="Job Failed" />
11 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
12 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
13 </stdio>
14 <command>
15 <![CDATA[
16 #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta"
17 #set $input_name = $s.display_name
18 #set $output_name = $input_name.replace(".mzML", "") + ".mzid"
19 ln -s '$s' '${input_name}' &&
20 ln -s '$d' '${db_name}' &&
21
22 java -jar \$(which MSGFPlus.jar)
23 -s '$input_name'
24 -d '$db_name'
25 -thread \${GALAXY_SLOTS:-1}
26
27 -tda $tda
28 -t $t$precursor_ion_tol_units
29 -ti $advanced.isotope_low,$advanced.isotope_high
30 -m $advanced.m
31 -inst $inst
32 -e $e
33 -protocol $advanced.protocol
34 -ntt $ntt
35 -minLength $advanced.minLength
36 -maxLength $advanced.maxLength
37 -minCharge $advanced.minCharge
38 -maxCharge $advanced.maxCharge
39 -n $advanced.n
40 -addFeatures $advanced.addFeatures
41 &&
42 mv '$output_name' output
43 ]]>
44 </command>
45 <inputs>
46 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
47 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
48 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
49 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
50 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
51 <option value="ppm" selected="true">Parts per million (ppm)</option>
52 <option value="Da">Daltons</option>
53 </param>
54 <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model">
55 <option value="0" selected="true">Low-res (LCQ/LTQ)</option>
56 <option value="1" >High-res (LTQ-Orbitrap)</option>
57 <option value="2" >Q-TOF</option>
58 <option value="3" >Q-Exactive</option>
59 </param>
60 <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme">
61 <option value="0">Unspecific cleavage</option>
62 <option value="1" selected="true">Trypsin, no P rule</option>
63 <option value="2">Chymotrypsin, no P rule (FYWL)</option>
64 <option value="3">Lys-C, no P rule</option>
65 <option value="4">Lys-N</option>
66 <option value="5">Glu-C (glutamyl endopeptidase)</option>
67 <option value="6">Arg-C</option>
68 <option value="7">Asp-N</option>
69 <option value="8">Alpha-lytic protease</option>
70 <option value="9">No enzyme</option>
71 </param>
72 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more.">
73 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option>
74 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option>
75 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
76 </param>
77 <!--
78 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
79 <options from_file="searchgui_mods.loc">
80 <column name="name" index="0" />
81 <column name="value" index="0" />
82 </options>
83 </param>
84 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
85 <options from_file="searchgui_mods.loc">
86 <column name="name" index="0" />
87 <column name="value" index="0" />
88 </options>
89 </param>-->
90
91 <!-- MS-GF+ ADVANCED PARAMETERS -->
92 <section name="advanced" title="Advanced Options">
93 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/>
94 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/>
95 <param argument="-minLength" label="Minimum peptide length" value="6" type="integer" help="Minimum peptide length to consider"/>
96 <param argument="-maxLength" label="Maximum peptide length" value="40" type="integer" help="Maximum peptide length to consider"/>
97 <param name="num_ptms" label="Maximum modifications allowed per peptide" type="integer" value="2" />
98 <param argument="-m" label="Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
99 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
100 <option value="1" >CID</option>
101 <option value="2" >ETD</option>
102 <option value="3" >HCD</option>
103 </param>
104 <param argument="-protocol" label="Protocol type" type="select" help="Protocols are used to enable scoring parameters for enriched and/or labeled samples">
105 <option value="0" selected="True">Automatic</option>
106 <option value="1" >Phosphorylation</option>
107 <option value="2" >iTRAQ</option>
108 <option value="3" >iTRAQPhospho</option>
109 <option value="4" >TMT</option>
110 <option value="5" >Standard</option>
111 </param>
112 <param argument="-n" label="Maximum matches per spectrum" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
113 <param argument="-addFeatures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" />
114 <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" />
115 <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" />
116 </section>
117 </inputs>
118 <outputs>
119 <data name="output" format="mzid" from_work_dir="output" />
120 </outputs>
121 <tests>
122 <test>
123 <param name="s" value="input/201208-378803.mzML" />
124 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
125 <output name="output" file="201208-378803-msgf.mzid" lines_diff="12" />
126 </test>
127 <test>
128 <param name="s" value="input/201208-378803.mzML" />
129 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
130 <param name="tda" value="1" />
131 <param name="t" value="0.02" />
132 <param name="precursor_ion_tol_units" value="Da" />
133 <param name="isotope_low" value="-1" />
134 <param name="isotope_high" value="0" />
135 <param name="m" value="1" />
136 <param name="inst" value="1" />
137 <param name="e" value="3" />
138 <param name="ntt" value="1" />
139 <param name="protocol" value="2" />
140 <param name="minLength" value="10" />
141 <param name="maxLength" value="20" />
142 <param name="minCharge" value="2" />
143 <param name="maxCharge" value="6" />
144 <param name="n" value="2" />
145 <param name="addFeatures" value="1" />
146 <output name="output" file="201208-378803-msgf-2mmu-semi-tryptic.mzid" lines_diff="12" />
147 </test>
148 </tests>
149 <help>
150 **What it does**
151
152 Performs protein identification via database search using MS-GF+.
153
154 </help>
155 <citations>
156 <citation type="doi">10.1038/ncomms6277</citation>
157 <citation type="doi">10.1021/pr8001244</citation>
158 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
159 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
160 </citations>
161 </tool>