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comparison TMTAnalyzer.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="TMTAnalyzer" name="TMTAnalyzer" 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 TMT quantitative values for peptides</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="TMTAnalyzer" name="TMTAnalyzer" version="2.0.0">
5 <token name="@EXECUTABLE@">TMTAnalyzer</token> 5 <description>Calculates TMT quantitative values for peptides</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">TMTAnalyzer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>TMTAnalyzer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>TMTAnalyzer
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_stats ${param_out_stats} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
16 -id_pool ${param_id_pool} 19 -out $param_out
17 -algorithm:Extraction:select_activation ${param_select_activation} 20 #end if
18 -algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift} 21 #if $param_out_mzq:
19 -algorithm:Extraction:channel_active ${param_channel_active} 22 -out_mzq $param_out_mzq
20 -algorithm:Quantification:channel_reference ${param_channel_reference} 23 #end if
24 #if $param_out_stats:
25 -out_stats $param_out_stats
26 #end if
27 -threads \${GALAXY_SLOTS:-24}
28 #if $param_algorithm_Extraction_select_activation:
29 -algorithm:Extraction:select_activation
30 #if &quot; &quot; in str($param_algorithm_Extraction_select_activation):
31 &quot;$param_algorithm_Extraction_select_activation&quot;
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 $rep_param_algorithm_Extraction_channel_active:
43 #if &quot; &quot; in str(token):
44 &quot;$token.param_algorithm_Extraction_channel_active&quot;
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
21 #if $adv_opts.adv_opts_selector=='advanced': 53 #if $adv_opts.adv_opts_selector=='advanced':
22 -out_mzq ${adv_opts.param_out_mzq} 54 #if $adv_opts.param_force:
23 -algorithm:Quantification:isotope_correction:tmt-6plex ${adv_opts.param_tmt-6plex} 55 -force
24 ${adv_opts.param_do_normalization} 56 #end if
25 -algorithm:MetaInformation:Program ${adv_opts.param_Program} 57
58 #if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
59 -algorithm:Quantification:isotope_correction:tmt-6plex
60 #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
61 #if &quot; &quot; in str(token):
62 &quot;$token.param_algorithm_Quantification_isotope_correction_tmt_6plex&quot;
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 $adv_opts.param_algorithm_MetaInformation_Program:
72 -algorithm:MetaInformation:Program &quot;$adv_opts.param_algorithm_MetaInformation_Program&quot;
73 #end if
26 #end if 74 #end if
27 </command> 75 </command>
28 <inputs> 76 <inputs>
29 <param name="param_in" type="data" format="mzML" optional="False" label="input raw/picked data file " help="(-in)"/> 77 <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/>
30 <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)"/> 78 <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">
31 <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)"> 79 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
32 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 80 <option value="Post-source decay">Post-source decay</option>
33 <option value="Post-source decay">Post-source decay</option> 81 <option value="Plasma desorption">Plasma desorption</option>
34 <option value="Plasma desorption">Plasma desorption</option> 82 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
35 <option value="Surface-induced dissociation">Surface-induced dissociation</option> 83 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
36 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> 84 <option value="Electron capture dissociation">Electron capture dissociation</option>
37 <option value="Electron capture dissociation">Electron capture dissociation</option> 85 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
38 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> 86 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
39 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> 87 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
40 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> 88 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
41 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> 89 <option value="Photodissociation">Photodissociation</option>
42 <option value="Photodissociation">Photodissociation</option> 90 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
43 <option value="Electron transfer dissociation">Electron transfer dissociation</option> 91 <option value=""></option>
44 <option value=""></option> 92 </param>
45 </param> 93 <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"/>
46 <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)"/> 94 <repeat max="1" min="0" name="rep_param_algorithm_Extraction_channel_active" title="param_algorithm_Extraction_channel_active">
47 <param name="param_channel_active" type="text" size="20" 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;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;." help="(-channel_active)"/> 95 <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 (126-131 for TMT-6-plex) in format &lt;channel&gt;:&lt;name&gt;," name="param_algorithm_Extraction_channel_active" size="30" type="text" value="126:liver 131:lung">
48 <param name="param_channel_reference" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)." help="(-channel_reference)"/> 96 <sanitizer>
49 <expand macro="advanced_options"> 97 <valid initial="string.printable">
50 <param name="param_tmt-6plex" type="text" size="20" 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; ; e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'." help="(-tmt-6plex)"/> 98 <remove value="'"/>
51 <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)"/> 99 <remove value="&quot;"/>
52 <param name="param_Program" type="text" size="20" value="OpenMS::TMTAnalyzer" label="" help="(-Program)"/> 100 </valid>
53 </expand> 101 </sanitizer>
54 </inputs> 102 </param>
55 <outputs> 103 </repeat>
56 <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/> 104 <param help="(-channel_reference) " label="Number of the reference channel (126-131)" max="131" min="126" name="param_algorithm_Quantification_channel_reference" optional="True" type="integer" value="126"/>
57 <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/> 105 <expand macro="advanced_options">
58 <data name="param_out_stats" label="output statistics as tab-separated file (readable by R or Excel or ...)" format="data"/> 106 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
59 </outputs> 107 <repeat max="1" min="0" name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" title="param_algorithm_Quantification_isotope_correction_tmt_6plex">
60 <help>**What it does** 108 <param help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'" 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_tmt_6plex" size="30" type="text" 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">
61 109 <sanitizer>
62 Calculates TMT quantitative values for peptides 110 <valid initial="string.printable">
111 <remove value="'"/>
112 <remove value="&quot;"/>
113 </valid>
114 </sanitizer>
115 </param>
116 </repeat>
117 <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"/>
118 <param help="(-Program) " label="" name="param_algorithm_MetaInformation_Program" size="30" type="text" value="OpenMS::TMTAnalyzer">
119 <sanitizer>
120 <valid initial="string.printable">
121 <remove value="'"/>
122 <remove value="&quot;"/>
123 </valid>
124 </sanitizer>
125 </param>
126 </expand>
127 </inputs>
128 <outputs>
129 <data format="consensusxml" name="param_out"/>
130 <data format="mzq" name="param_out_mzq"/>
131 <data format="tabular" name="param_out_stats"/>
132 </outputs>
133 <help>Calculates TMT quantitative values for peptides
63 134
64 135
65 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html 136 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help>
66 137 </tool>
67 @REFERENCES@
68 </help>
69 </tool>