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comparison IDMassAccuracy.xml @ 0:f0fedc21f90b 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 12:24:31 -0500
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children 49dcff453eee
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-1:000000000000 0:f0fedc21f90b
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: [Utilities]-->
4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.1.0">
5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
6 <macros>
7 <token name="@EXECUTABLE@">IDMassAccuracy</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDMassAccuracy
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 -id_in
20 #for token in $param_id_in:
21 $token
22 #end for
23 #if $param_precursor_out:
24 -precursor_out $param_precursor_out
25 #end if
26
27 #if $rep_param_precursor_columns:
28 -precursor_columns
29 #for token in $rep_param_precursor_columns:
30 #if " " in str(token):
31 "$token.param_precursor_columns"
32 #else
33 $token.param_precursor_columns
34 #end if
35 #end for
36 #end if
37 #if $param_precursor_error_ppm:
38 -precursor_error_ppm
39 #end if
40 #if $param_fragment_out:
41 -fragment_out $param_fragment_out
42 #end if
43
44 #if $rep_param_fragment_columns:
45 -fragment_columns
46 #for token in $rep_param_fragment_columns:
47 #if " " in str(token):
48 "$token.param_fragment_columns"
49 #else
50 $token.param_fragment_columns
51 #end if
52 #end for
53 #end if
54 #if $param_fragment_error_ppm:
55 -fragment_error_ppm
56 #end if
57 #if $param_fragment_mass_tolerance:
58 -fragment_mass_tolerance $param_fragment_mass_tolerance
59 #end if
60 #if $param_separator:
61 -separator "$param_separator"
62 #end if
63 #if $adv_opts.adv_opts_selector=='advanced':
64 #if $adv_opts.param_number_of_bins:
65 -number_of_bins $adv_opts.param_number_of_bins
66 #end if
67 #if $adv_opts.param_generate_gnuplot_scripts:
68 -generate_gnuplot_scripts
69 #end if
70 #if $adv_opts.param_force:
71 -force
72 #end if
73 #end if
74 </command>
75 <inputs>
76 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) ">
77 <sanitizer>
78 <valid initial="string.printable">
79 <remove value="'"/>
80 <remove value="&quot;"/>
81 </valid>
82 </sanitizer>
83 </param>
84 <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) ">
85 <sanitizer>
86 <valid initial="string.printable">
87 <remove value="'"/>
88 <remove value="&quot;"/>
89 </valid>
90 </sanitizer>
91 </param>
92 <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns">
93 <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) ">
94 <option value="MassDifference">MassDifference</option>
95 </param>
96 </repeat>
97 <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/>
98 <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns">
99 <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) ">
100 <option value="MassDifference">MassDifference</option>
101 </param>
102 </repeat>
103 <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/>
104 <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/>
105 <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) ">
106 <sanitizer>
107 <valid initial="string.printable">
108 <remove value="'"/>
109 <remove value="&quot;"/>
110 </valid>
111 </sanitizer>
112 </param>
113 <expand macro="advanced_options">
114 <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/>
115 <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/>
116 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
117 </expand>
118 </inputs>
119 <outputs>
120 <data name="param_precursor_out" format="tabular"/>
121 <data name="param_fragment_out" format="tabular"/>
122 </outputs>
123 <help>Calculates a distribution of the mass error from given mass spectra and IDs.
124
125
126 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help>
127 </tool>