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comparison OpenSwathAssayGenerator.xml @ 0:c5136f02a0fa draft

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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 12:22:47 -0500
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children 1c46da1a81a7
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-1:000000000000 0:c5136f02a0fa
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: [Targeted Experiments]-->
4 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="2.1.0">
5 <description>Generates assays according to different models for a specific TraML</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathAssayGenerator
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_min_transitions:
22 -min_transitions $param_min_transitions
23 #end if
24 #if $param_max_transitions:
25 -max_transitions $param_max_transitions
26 #end if
27 #if $param_allowed_fragment_types:
28 -allowed_fragment_types "$param_allowed_fragment_types"
29 #end if
30 #if $param_allowed_fragment_charges:
31 -allowed_fragment_charges "$param_allowed_fragment_charges"
32 #end if
33 #if $param_enable_detection_specific_losses:
34 -enable_detection_specific_losses
35 #end if
36 #if $param_enable_detection_unspecific_losses:
37 -enable_detection_unspecific_losses
38 #end if
39 #if $param_enable_identification_specific_losses:
40 -enable_identification_specific_losses
41 #end if
42 #if $param_enable_identification_unspecific_losses:
43 -enable_identification_unspecific_losses
44 #end if
45 #if $param_enable_identification_ms2_precursors:
46 -enable_identification_ms2_precursors
47 #end if
48 #if $param_enable_ms1_uis_scoring:
49 -enable_ms1_uis_scoring
50 #end if
51 #if $param_enable_ms2_uis_scoring:
52 -enable_ms2_uis_scoring
53 #end if
54 #if $param_max_num_alternative_localizations:
55 -max_num_alternative_localizations $param_max_num_alternative_localizations
56 #end if
57 #if $param_enable_reannotation:
58 -enable_reannotation
59 #end if
60 #if $param_precursor_mz_threshold:
61 -precursor_mz_threshold $param_precursor_mz_threshold
62 #end if
63 #if $param_precursor_lower_mz_limit:
64 -precursor_lower_mz_limit $param_precursor_lower_mz_limit
65 #end if
66 #if $param_precursor_upper_mz_limit:
67 -precursor_upper_mz_limit $param_precursor_upper_mz_limit
68 #end if
69 #if $param_product_mz_threshold:
70 -product_mz_threshold $param_product_mz_threshold
71 #end if
72 #if $param_product_lower_mz_limit:
73 -product_lower_mz_limit $param_product_lower_mz_limit
74 #end if
75 #if $param_product_upper_mz_limit:
76 -product_upper_mz_limit $param_product_upper_mz_limit
77 #end if
78 #if $adv_opts.adv_opts_selector=='advanced':
79 #if $adv_opts.param_swath_windows_file:
80 -swath_windows_file $adv_opts.param_swath_windows_file
81 #end if
82 #if $adv_opts.param_force:
83 -force
84 #end if
85 #end if
86 </command>
87 <inputs>
88 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
89 <param name="param_min_transitions" type="integer" value="6" label="minimal number of transitions" help="(-min_transitions) "/>
90 <param name="param_max_transitions" type="integer" value="6" label="maximal number of transitions" help="(-max_transitions) "/>
91 <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) ">
92 <sanitizer>
93 <valid initial="string.printable">
94 <remove value="'"/>
95 <remove value="&quot;"/>
96 </valid>
97 </sanitizer>
98 </param>
99 <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) ">
100 <sanitizer>
101 <valid initial="string.printable">
102 <remove value="'"/>
103 <remove value="&quot;"/>
104 </valid>
105 </sanitizer>
106 </param>
107 <param name="param_enable_detection_specific_losses" display="radio" type="boolean" truevalue="-enable_detection_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help="(-enable_detection_specific_losses) "/>
108 <param name="param_enable_detection_unspecific_losses" display="radio" type="boolean" truevalue="-enable_detection_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help="(-enable_detection_unspecific_losses) "/>
109 <param name="param_enable_identification_specific_losses" display="radio" type="boolean" truevalue="-enable_identification_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for identification fragment ions should be allowed" help="(-enable_identification_specific_losses) "/>
110 <param name="param_enable_identification_unspecific_losses" display="radio" type="boolean" truevalue="-enable_identification_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help="(-enable_identification_unspecific_losses) "/>
111 <param name="param_enable_identification_ms2_precursors" display="radio" type="boolean" truevalue="-enable_identification_ms2_precursors" falsevalue="" checked="false" optional="True" label="set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level)" help="(-enable_identification_ms2_precursors) This may help in identification if the MS1 signal is weak"/>
112 <param name="param_enable_ms1_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms1_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS1-UIS assays for UIS scoring should be generated" help="(-enable_ms1_uis_scoring) "/>
113 <param name="param_enable_ms2_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms2_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS2-UIS assays for UIS scoring should be generated" help="(-enable_ms2_uis_scoring) "/>
114 <param name="param_max_num_alternative_localizations" type="integer" value="20" label="maximum number of site-localization permutations" help="(-max_num_alternative_localizations) "/>
115 <param name="param_enable_reannotation" display="radio" type="boolean" truevalue="-enable_reannotation" falsevalue="" checked="false" optional="True" label="set this flag if reannotation of fragment ions should be allowed" help="(-enable_reannotation) "/>
116 <param name="param_precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help="(-precursor_mz_threshold) "/>
117 <param name="param_precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help="(-precursor_lower_mz_limit) "/>
118 <param name="param_precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help="(-precursor_upper_mz_limit) "/>
119 <param name="param_product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help="(-product_mz_threshold) "/>
120 <param name="param_product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help="(-product_lower_mz_limit) "/>
121 <param name="param_product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help="(-product_upper_mz_limit) "/>
122 <expand macro="advanced_options">
123 <param name="param_swath_windows_file" type="data" format="txt" optional="True" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
124 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
125 </expand>
126 </inputs>
127 <outputs>
128 <data name="param_out" format="traml"/>
129 </outputs>
130 <help>Generates assays according to different models for a specific TraML
131
132
133 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAssayGenerator.html</help>
134 </tool>