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comparison ITRAQAnalyzer.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="ITRAQAnalyzer" name="ITRAQAnalyzer" version="1.12.0"> 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 <description>Calculates iTRAQ quantitative values for peptides</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="ITRAQAnalyzer" name="ITRAQAnalyzer" version="2.0.0">
5 <token name="@EXECUTABLE@">ITRAQAnalyzer</token> 5 <description>Calculates iTRAQ quantitative values for peptides</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">ITRAQAnalyzer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>ITRAQAnalyzer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ITRAQAnalyzer
11 14
12 -type ${param_type} 15 #if $param_type:
13 -in ${param_in} 16 -type
14 -out ${param_out} 17 #if &quot; &quot; in str($param_type):
15 -out_stats ${param_out_stats} 18 &quot;$param_type&quot;
16 -threads \${GALAXY_SLOTS:-24} 19 #else
17 -id_pool ${param_id_pool} 20 $param_type
18 -algorithm:Extraction:select_activation ${param_select_activation} 21 #end if
19 -algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift} 22 #end if
20 -algorithm:Extraction:channel_active ${param_channel_active} 23 #if $param_in:
21 -algorithm:Quantification:channel_reference ${param_channel_reference} 24 -in $param_in
25 #end if
26 #if $param_out:
27 -out $param_out
28 #end if
29 #if $param_out_mzq:
30 -out_mzq $param_out_mzq
31 #end if
32 #if $param_out_stats:
33 -out_stats $param_out_stats
34 #end if
35 -threads \${GALAXY_SLOTS:-24}
36 #if $param_algorithm_Extraction_select_activation:
37 -algorithm:Extraction:select_activation
38 #if &quot; &quot; in str($param_algorithm_Extraction_select_activation):
39 &quot;$param_algorithm_Extraction_select_activation&quot;
40 #else
41 $param_algorithm_Extraction_select_activation
42 #end if
43 #end if
44 #if $param_algorithm_Extraction_reporter_mass_shift:
45 -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
46 #end if
47
48 #if $rep_param_algorithm_Extraction_channel_active:
49 -algorithm:Extraction:channel_active
50 #for token in $rep_param_algorithm_Extraction_channel_active:
51 #if &quot; &quot; in str(token):
52 &quot;$token.param_algorithm_Extraction_channel_active&quot;
53 #else
54 $token.param_algorithm_Extraction_channel_active
55 #end if
56 #end for
57 #end if
58 #if $param_algorithm_Quantification_channel_reference:
59 -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
60 #end if
22 #if $adv_opts.adv_opts_selector=='advanced': 61 #if $adv_opts.adv_opts_selector=='advanced':
23 -out_mzq ${adv_opts.param_out_mzq} 62 #if $adv_opts.param_force:
24 -algorithm:Quantification:isotope_correction:4plex ${adv_opts.param_4plex} 63 -force
25 -algorithm:Quantification:isotope_correction:8plex ${adv_opts.param_8plex} 64 #end if
26 ${adv_opts.param_do_normalization} 65
27 -algorithm:MetaInformation:Program ${adv_opts.param_Program} 66 #if $rep_param_algorithm_Quantification_isotope_correction_4plex:
67 -algorithm:Quantification:isotope_correction:4plex
68 #for token in $rep_param_algorithm_Quantification_isotope_correction_4plex:
69 #if &quot; &quot; in str(token):
70 &quot;$token.param_algorithm_Quantification_isotope_correction_4plex&quot;
71 #else
72 $token.param_algorithm_Quantification_isotope_correction_4plex
73 #end if
74 #end for
75 #end if
76
77 #if $rep_param_algorithm_Quantification_isotope_correction_8plex:
78 -algorithm:Quantification:isotope_correction:8plex
79 #for token in $rep_param_algorithm_Quantification_isotope_correction_8plex:
80 #if &quot; &quot; in str(token):
81 &quot;$token.param_algorithm_Quantification_isotope_correction_8plex&quot;
82 #else
83 $token.param_algorithm_Quantification_isotope_correction_8plex
84 #end if
85 #end for
86 #end if
87 #if $adv_opts.param_algorithm_Quantification_do_normalization:
88 -algorithm:Quantification:do_normalization
89 #end if
90 #if $adv_opts.param_algorithm_MetaInformation_Program:
91 -algorithm:MetaInformation:Program &quot;$adv_opts.param_algorithm_MetaInformation_Program&quot;
92 #end if
28 #end if 93 #end if
29 </command> 94 </command>
30 <inputs> 95 <inputs>
31 <param name="param_type" type="select" optional="True" value="4plex" label="iTRAQ experiment type#br#" help="(-type)"> 96 <param help="(-type) " label="iTRAQ experiment type" name="param_type" optional="True" type="select" value="4plex">
32 <option value="4plex">4plex</option> 97 <option value="4plex">4plex</option>
33 <option value="8plex">8plex</option> 98 <option value="8plex">8plex</option>
34 </param> 99 </param>
35 <param name="param_in" type="data" format="mzML" optional="False" label="input raw/picked data file " help="(-in)"/> 100 <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/>
36 <param name="param_id_pool" type="text" size="20" label="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /home/thouwaar/Projects/OpenMS/share/OpenMS/IDPool/IDPool.txt)" help="(-id_pool)"/> 101 <param help="(-select_activation) Set to empty string if you want to disable filtering" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" name="param_algorithm_Extraction_select_activation" optional="True" type="select" value="High-energy collision-induced dissociation">
37 <param name="param_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). Set to empty string if you want to disable filtering." help="(-select_activation)"> 102 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
38 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 103 <option value="Post-source decay">Post-source decay</option>
39 <option value="Post-source decay">Post-source decay</option> 104 <option value="Plasma desorption">Plasma desorption</option>
40 <option value="Plasma desorption">Plasma desorption</option> 105 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
41 <option value="Surface-induced dissociation">Surface-induced dissociation</option> 106 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
42 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> 107 <option value="Electron capture dissociation">Electron capture dissociation</option>
43 <option value="Electron capture dissociation">Electron capture dissociation</option> 108 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
44 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> 109 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
45 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> 110 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
46 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> 111 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
47 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> 112 <option value="Photodissociation">Photodissociation</option>
48 <option value="Photodissociation">Photodissociation</option> 113 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
49 <option value="Electron transfer dissociation">Electron transfer dissociation</option> 114 <option value=""></option>
50 <option value=""></option> 115 </param>
51 </param> 116 <param help="(-reporter_mass_shift) " label="Allowed shift (left to right) in Da from the expected position" max="0.5" min="1e-08" name="param_algorithm_Extraction_reporter_mass_shift" optional="True" type="float" value="0.1"/>
52 <param name="param_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 max="1" min="0" name="rep_param_algorithm_Extraction_channel_active" title="param_algorithm_Extraction_channel_active">
53 <param name="param_channel_active" type="text" size="20" 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;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;." help="(-channel_active)"/> 118 <param help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;" 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;," name="param_algorithm_Extraction_channel_active" size="30" type="text" value="114:liver 117:lung">
54 <param name="param_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)"/> 119 <sanitizer>
55 <expand macro="advanced_options"> 120 <valid initial="string.printable">
56 <param name="param_4plex" type="text" size="20" 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; ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'." help="(-4plex)"/> 121 <remove value="'"/>
57 <param name="param_8plex" type="text" size="20" 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; ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'." help="(-8plex)"/> 122 <remove value="&quot;"/>
58 <param name="param_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization true" falsevalue="-algorithm:Quantification:do_normalization false" checked="false" optional="True" label="Normalize channels? 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!" help="(-do_normalization)"/> 123 </valid>
59 <param name="param_Program" type="text" size="20" value="OpenMS::ITRAQAnalyzer" label="" help="(-Program)"/> 124 </sanitizer>
60 </expand> 125 </param>
61 </inputs> 126 </repeat>
62 <outputs> 127 <param help="(-channel_reference) " label="Number of the reference channel (114-117 for 4plex)" max="117" min="114" name="param_algorithm_Quantification_channel_reference" optional="True" type="integer" value="114"/>
63 <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/> 128 <expand macro="advanced_options">
64 <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/> 129 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
65 <data name="param_out_stats" label="output statistics as tab-separated file (readable by R or Excel or ...)" format="data"/> 130 <repeat max="1" min="0" name="rep_param_algorithm_Quantification_isotope_correction_4plex" title="param_algorithm_Quantification_isotope_correction_4plex">
66 </outputs> 131 <param help="(-4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'" 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; ;" name="param_algorithm_Quantification_isotope_correction_4plex" size="30" type="text" 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">
67 <help>**What it does** 132 <sanitizer>
68 133 <valid initial="string.printable">
69 Calculates iTRAQ quantitative values for peptides 134 <remove value="'"/>
135 <remove value="&quot;"/>
136 </valid>
137 </sanitizer>
138 </param>
139 </repeat>
140 <repeat max="1" min="0" name="rep_param_algorithm_Quantification_isotope_correction_8plex" title="param_algorithm_Quantification_isotope_correction_8plex">
141 <param help="(-8plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'" 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; ;" name="param_algorithm_Quantification_isotope_correction_8plex" size="30" type="text" 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">
142 <sanitizer>
143 <valid initial="string.printable">
144 <remove value="'"/>
145 <remove value="&quot;"/>
146 </valid>
147 </sanitizer>
148 </param>
149 </repeat>
150 <param checked="false" falsevalue="" 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!" label="Normalize channels?" name="param_algorithm_Quantification_do_normalization" optional="True" truevalue="-algorithm:Quantification:do_normalization" type="boolean"/>
151 <param help="(-Program) " label="" name="param_algorithm_MetaInformation_Program" size="30" type="text" value="OpenMS::ITRAQAnalyzer">
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 format="consensusxml" name="param_out"/>
163 <data format="mzq" name="param_out_mzq"/>
164 <data format="tabular" name="param_out_stats"/>
165 </outputs>
166 <help>Calculates iTRAQ quantitative values for peptides
70 167
71 168
72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html 169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html</help>
73 170 </tool>
74 @REFERENCES@
75 </help>
76 </tool>