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comparison ITRAQAnalyzer.xml @ 0:014f4e11a3d9 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:56:52 -0500
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-1:000000000000 0:014f4e11a3d9
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ITRAQAnalyzer" name="ITRAQAnalyzer" version="2.1.0">
5 <description>Calculates iTRAQ quantitative values for peptides</description>
6 <macros>
7 <token name="@EXECUTABLE@">ITRAQAnalyzer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ITRAQAnalyzer
14
15 #if $param_type:
16 -type $param_type
17 #end if
18 #if $param_in:
19 -in $param_in
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_out_mzq:
25 -out_mzq $param_out_mzq
26 #end if
27 #if $param_out_stats:
28 -out_stats $param_out_stats
29 #end if
30 #if $param_id_pool:
31 -id_pool "$param_id_pool"
32 #end if
33 #if $param_algorithm_Extraction_select_activation:
34 -algorithm:Extraction:select_activation $param_algorithm_Extraction_select_activation
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_4plex:
59 -algorithm:Quantification:isotope_correction:4plex
60 #for token in $rep_param_algorithm_Quantification_isotope_correction_4plex:
61 #if " " in str(token):
62 "$token.param_algorithm_Quantification_isotope_correction_4plex"
63 #else
64 $token.param_algorithm_Quantification_isotope_correction_4plex
65 #end if
66 #end for
67 #end if
68
69 #if $rep_param_algorithm_Quantification_isotope_correction_8plex:
70 -algorithm:Quantification:isotope_correction:8plex
71 #for token in $rep_param_algorithm_Quantification_isotope_correction_8plex:
72 #if " " in str(token):
73 "$token.param_algorithm_Quantification_isotope_correction_8plex"
74 #else
75 $token.param_algorithm_Quantification_isotope_correction_8plex
76 #end if
77 #end for
78 #end if
79 #if $adv_opts.param_algorithm_Quantification_do_normalization:
80 -algorithm:Quantification:do_normalization
81 #end if
82 #if $adv_opts.param_algorithm_MetaInformation_Program:
83 -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program"
84 #end if
85 #end if
86 </command>
87 <inputs>
88 <param name="param_type" display="radio" type="select" optional="False" value="4plex" label="iTRAQ experiment type" help="(-type) ">
89 <option value="4plex" selected="true">4plex</option>
90 <option value="8plex">8plex</option>
91 </param>
92 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
93 <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/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)">
94 <sanitizer>
95 <valid initial="string.printable">
96 <remove value="'"/>
97 <remove value="&quot;"/>
98 </valid>
99 </sanitizer>
100 </param>
101 <param name="param_algorithm_Extraction_select_activation" type="select" optional="False" 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">
102 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
103 <option value="Post-source decay">Post-source decay</option>
104 <option value="Plasma desorption">Plasma desorption</option>
105 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
106 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
107 <option value="Electron capture dissociation">Electron capture dissociation</option>
108 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
109 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
110 <option value="High-energy collision-induced dissociation" selected="true">High-energy collision-induced dissociation</option>
111 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
112 <option value="Photodissociation">Photodissociation</option>
113 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
114 <option value=""></option>
115 </param>
116 <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) "/>
117 <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active">
118 <param name="param_algorithm_Extraction_channel_active" type="text" size="30" value="114:liver 117:lung" label="Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;">
119 <sanitizer>
120 <valid initial="string.printable">
121 <remove value="'"/>
122 <remove value="&quot;"/>
123 </valid>
124 </sanitizer>
125 </param>
126 </repeat>
127 <param name="param_algorithm_Quantification_channel_reference" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117 for 4plex)" help="(-channel_reference) "/>
128 <expand macro="advanced_options">
129 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
130 <repeat name="rep_param_algorithm_Quantification_isotope_correction_4plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_4plex">
131 <param name="param_algorithm_Quantification_isotope_correction_4plex" type="text" size="30" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1" 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="(-4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'">
132 <sanitizer>
133 <valid initial="string.printable">
134 <remove value="'"/>
135 <remove value="&quot;"/>
136 </valid>
137 </sanitizer>
138 </param>
139 </repeat>
140 <repeat name="rep_param_algorithm_Quantification_isotope_correction_8plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_8plex">
141 <param name="param_algorithm_Quantification_isotope_correction_8plex" type="text" size="30" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0" 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="(-8plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'">
142 <sanitizer>
143 <valid initial="string.printable">
144 <remove value="'"/>
145 <remove value="&quot;"/>
146 </valid>
147 </sanitizer>
148 </param>
149 </repeat>
150 <param name="param_algorithm_Quantification_do_normalization" display="radio" 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!"/>
151 <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::ITRAQAnalyzer" label="" help="(-Program) ">
152 <sanitizer>
153 <valid initial="string.printable">
154 <remove value="'"/>
155 <remove value="&quot;"/>
156 </valid>
157 </sanitizer>
158 </param>
159 </expand>
160 </inputs>
161 <outputs>
162 <data name="param_out" format="consensusxml"/>
163 <data name="param_out_mzq" format="mzq"/>
164 <data name="param_out_stats" format="tabular"/>
165 </outputs>
166 <help>Calculates iTRAQ quantitative values for peptides
167
168
169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html</help>
170 </tool>