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comparison TMTAnalyzer.xml @ 0:d05c7c810dd8 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 12:32:02 -0500
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-1:000000000000 0:d05c7c810dd8
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="TMTAnalyzer" name="TMTAnalyzer" version="2.1.0">
5 <description>Calculates TMT quantitative values for peptides</description>
6 <macros>
7 <token name="@EXECUTABLE@">TMTAnalyzer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>TMTAnalyzer
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_out_mzq:
22 -out_mzq $param_out_mzq
23 #end if
24 #if $param_out_stats:
25 -out_stats $param_out_stats
26 #end if
27 #if $param_id_pool:
28 -id_pool "$param_id_pool"
29 #end if
30 #if $param_algorithm_Extraction_select_activation:
31 -algorithm:Extraction:select_activation $param_algorithm_Extraction_select_activation
32 #end if
33 #if $param_algorithm_Extraction_reporter_mass_shift:
34 -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
35 #end if
36
37 #if $rep_param_algorithm_Extraction_channel_active:
38 -algorithm:Extraction:channel_active
39 #for token in $rep_param_algorithm_Extraction_channel_active:
40 #if " " in str(token):
41 "$token.param_algorithm_Extraction_channel_active"
42 #else
43 $token.param_algorithm_Extraction_channel_active
44 #end if
45 #end for
46 #end if
47 #if $param_algorithm_Quantification_channel_reference:
48 -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
49 #end if
50 #if $adv_opts.adv_opts_selector=='advanced':
51 #if $adv_opts.param_force:
52 -force
53 #end if
54
55 #if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
56 -algorithm:Quantification:isotope_correction:tmt-6plex
57 #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
58 #if " " in str(token):
59 "$token.param_algorithm_Quantification_isotope_correction_tmt_6plex"
60 #else
61 $token.param_algorithm_Quantification_isotope_correction_tmt_6plex
62 #end if
63 #end for
64 #end if
65 #if $adv_opts.param_algorithm_Quantification_do_normalization:
66 -algorithm:Quantification:do_normalization
67 #end if
68 #if $adv_opts.param_algorithm_MetaInformation_Program:
69 -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program"
70 #end if
71 #end if
72 </command>
73 <inputs>
74 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
75 <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)">
76 <sanitizer>
77 <valid initial="string.printable">
78 <remove value="'"/>
79 <remove value="&quot;"/>
80 </valid>
81 </sanitizer>
82 </param>
83 <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">
84 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
85 <option value="Post-source decay">Post-source decay</option>
86 <option value="Plasma desorption">Plasma desorption</option>
87 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
88 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
89 <option value="Electron capture dissociation">Electron capture dissociation</option>
90 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
91 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
92 <option value="High-energy collision-induced dissociation" selected="true">High-energy collision-induced dissociation</option>
93 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
94 <option value="Photodissociation">Photodissociation</option>
95 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
96 <option value=""></option>
97 </param>
98 <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) "/>
99 <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active">
100 <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;">
101 <sanitizer>
102 <valid initial="string.printable">
103 <remove value="'"/>
104 <remove value="&quot;"/>
105 </valid>
106 </sanitizer>
107 </param>
108 </repeat>
109 <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) "/>
110 <expand macro="advanced_options">
111 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
112 <repeat name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_tmt_6plex">
113 <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'">
114 <sanitizer>
115 <valid initial="string.printable">
116 <remove value="'"/>
117 <remove value="&quot;"/>
118 </valid>
119 </sanitizer>
120 </param>
121 </repeat>
122 <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!"/>
123 <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::TMTAnalyzer" label="" help="(-Program) ">
124 <sanitizer>
125 <valid initial="string.printable">
126 <remove value="'"/>
127 <remove value="&quot;"/>
128 </valid>
129 </sanitizer>
130 </param>
131 </expand>
132 </inputs>
133 <outputs>
134 <data name="param_out" format="consensusxml"/>
135 <data name="param_out_mzq" format="mzq"/>
136 <data name="param_out_stats" format="tabular"/>
137 </outputs>
138 <help>Calculates TMT quantitative values for peptides
139
140
141 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help>
142 </tool>