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comparison IDMassAccuracy.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
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3:ec62782f6c68 4:6ead64a594bd
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="2.0.0">
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 $rep_param_precursor_columns:
30 #if &quot; &quot; in str(token):
31 &quot;$token.param_precursor_columns&quot;
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 $rep_param_fragment_columns:
47 #if &quot; &quot; in str(token):
48 &quot;$token.param_fragment_columns&quot;
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 $param_separator:
61 -separator &quot;$param_separator&quot;
62 #end if
63 -threads \${GALAXY_SLOTS:-24}
64 #if $adv_opts.adv_opts_selector=='advanced':
65 #if $adv_opts.param_number_of_bins:
66 -number_of_bins $adv_opts.param_number_of_bins
67 #end if
68 #if $adv_opts.param_generate_gnuplot_scripts:
69 -generate_gnuplot_scripts
70 #end if
71 #if $adv_opts.param_force:
72 -force
73 #end if
74 #end if
75 </command>
76 <inputs>
77 <param format="mzml" help="(-in) " label="Input mzML file list, containing the spectra" multiple="true" name="param_in" optional="False" size="30" type="data">
78 <sanitizer>
79 <valid initial="string.printable">
80 <remove value="'"/>
81 <remove value="&quot;"/>
82 </valid>
83 </sanitizer>
84 </param>
85 <param format="xml" help="(-id_in) " label="Input idXML file list, containing the identifications" multiple="true" name="param_id_in" optional="False" size="30" type="data">
86 <sanitizer>
87 <valid initial="string.printable">
88 <remove value="'"/>
89 <remove value="&quot;"/>
90 </valid>
91 </sanitizer>
92 </param>
93 <repeat max="1" min="0" name="rep_param_precursor_columns" title="param_precursor_columns">
94 <param help="(-precursor_columns) " label="Columns which will be written to the output file" name="param_precursor_columns" size="30" type="text" value="MassDifference">
95 <sanitizer>
96 <valid initial="string.printable">
97 <remove value="'"/>
98 <remove value="&quot;"/>
99 </valid>
100 </sanitizer>
101 </param>
102 </repeat>
103 <param checked="false" falsevalue="" help="(-precursor_error_ppm) " label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" name="param_precursor_error_ppm" optional="True" truevalue="-precursor_error_ppm" type="boolean"/>
104 <repeat max="1" min="0" name="rep_param_fragment_columns" title="param_fragment_columns">
105 <param help="(-fragment_columns) " label="Columns which will be written to the output file" name="param_fragment_columns" size="30" type="text" value="MassDifference">
106 <sanitizer>
107 <valid initial="string.printable">
108 <remove value="'"/>
109 <remove value="&quot;"/>
110 </valid>
111 </sanitizer>
112 </param>
113 </repeat>
114 <param checked="false" falsevalue="" help="(-fragment_error_ppm) " label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" name="param_fragment_error_ppm" optional="True" truevalue="-fragment_error_ppm" type="boolean"/>
115 <param help="(-fragment_mass_tolerance) " label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" name="param_fragment_mass_tolerance" type="float" value="0.5"/>
116 <param help="(-separator) " label="character which should be used to separate the columns in the output files" name="param_separator" size="30" type="text" value=" ">
117 <sanitizer>
118 <valid initial="string.printable">
119 <remove value="'"/>
120 <remove value="&quot;"/>
121 </valid>
122 </sanitizer>
123 </param>
124 <expand macro="advanced_options">
125 <param help="(-number_of_bins) " label="Number of bins that should be used to calculate the histograms for the fitting" min="10" name="param_number_of_bins" optional="True" type="integer" value="100"/>
126 <param checked="false" falsevalue="" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect" 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" name="param_generate_gnuplot_scripts" optional="True" truevalue="-generate_gnuplot_scripts" type="boolean"/>
127 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
128 </expand>
129 </inputs>
130 <outputs>
131 <data format="tabular" name="param_precursor_out"/>
132 <data format="tabular" name="param_fragment_out"/>
133 </outputs>
134 <help>Calculates a distribution of the mass error from given mass spectra and IDs.
135
136
137 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help>
138 </tool>