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comparison TMTAnalyzer.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="TMTAnalyzer" name="TMTAnalyzer" version="2.0.0">
3 <description>Calculates TMT quantitative values for peptides</description>
4 <macros>
5 <token name="@EXECUTABLE@">TMTAnalyzer</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>TMTAnalyzer
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_out_mzq:
19 -out_mzq $param_out_mzq
20 #end if
21 #if $param_out_stats:
22 -out_stats $param_out_stats
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $param_id_pool:
26 -id_pool "$param_id_pool"
27 #end if
28 #if $param_algorithm_Extraction_select_activation:
29 -algorithm:Extraction:select_activation
30 #if " " in str($param_algorithm_Extraction_select_activation):
31 "$param_algorithm_Extraction_select_activation"
32 #else
33 $param_algorithm_Extraction_select_activation
34 #end if
35 #end if
36 #if $param_algorithm_Extraction_reporter_mass_shift:
37 -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
38 #end if
39
40 #if $rep_param_algorithm_Extraction_channel_active:
41 -algorithm:Extraction:channel_active
42 #for token in $rep_param_algorithm_Extraction_channel_active:
43 #if " " in str(token):
44 "$token.param_algorithm_Extraction_channel_active"
45 #else
46 $token.param_algorithm_Extraction_channel_active
47 #end if
48 #end for
49 #end if
50 #if $param_algorithm_Quantification_channel_reference:
51 -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
52 #end if
53 #if $adv_opts.adv_opts_selector=='advanced':
54 #if $adv_opts.param_force:
55 -force
56 #end if
57
58 #if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
59 -algorithm:Quantification:isotope_correction:tmt-6plex
60 #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
61 #if " " in str(token):
62 "$token.param_algorithm_Quantification_isotope_correction_tmt_6plex"
63 #else
64 $token.param_algorithm_Quantification_isotope_correction_tmt_6plex
65 #end if
66 #end for
67 #end if
68 #if $adv_opts.param_algorithm_Quantification_do_normalization:
69 -algorithm:Quantification:do_normalization
70 #end if
71 #if $adv_opts.param_algorithm_MetaInformation_Program:
72 -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program"
73 #end if
74 #end if
75 </command>
76 <inputs>
77 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
78 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/thouwaar/Downloads/openms-2.0-Linux-x86_64/share/OpenMS/IDPool/IDPool.txt)">
79 <sanitizer>
80 <valid initial="string.printable">
81 <remove value="'"/>
82 <remove value="&quot;"/>
83 </valid>
84 </sanitizer>
85 </param>
86 <param name="param_algorithm_Extraction_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" help="(-select_activation) Set to empty string if you want to disable filtering">
87 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
88 <option value="Post-source decay">Post-source decay</option>
89 <option value="Plasma desorption">Plasma desorption</option>
90 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
91 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
92 <option value="Electron capture dissociation">Electron capture dissociation</option>
93 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
94 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
95 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
96 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
97 <option value="Photodissociation">Photodissociation</option>
98 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
99 <option value=""></option>
100 </param>
101 <param name="param_algorithm_Extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/>
102 <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active">
103 <param name="param_algorithm_Extraction_channel_active" type="text" size="30" value="126:liver 131:lung" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;">
104 <sanitizer>
105 <valid initial="string.printable">
106 <remove value="'"/>
107 <remove value="&quot;"/>
108 </valid>
109 </sanitizer>
110 </param>
111 </repeat>
112 <param name="param_algorithm_Quantification_channel_reference" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-channel_reference) "/>
113 <expand macro="advanced_options">
114 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
115 <repeat name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_tmt_6plex">
116 <param name="param_algorithm_Quantification_isotope_correction_tmt_6plex" type="text" size="30" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0" label="Override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'">
117 <sanitizer>
118 <valid initial="string.printable">
119 <remove value="'"/>
120 <remove value="&quot;"/>
121 </valid>
122 </sanitizer>
123 </param>
124 </repeat>
125 <param name="param_algorithm_Quantification_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization" falsevalue="" checked="false" optional="True" label="Normalize channels?" help="(-do_normalization) Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/>
126 <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::TMTAnalyzer" label="" help="(-Program) ">
127 <sanitizer>
128 <valid initial="string.printable">
129 <remove value="'"/>
130 <remove value="&quot;"/>
131 </valid>
132 </sanitizer>
133 </param>
134 </expand>
135 </inputs>
136 <outputs>
137 <data name="param_out" format="consensusxml"/>
138 <data name="param_out_mzq" format="mzq"/>
139 <data name="param_out_stats" format="tabular"/>
140 </outputs>
141 <help>**What it does**
142
143 Calculates TMT quantitative values for peptides
144
145
146 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help>
147 <expand macro="references"/>
148 </tool>