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comparison InternalCalibration.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="InternalCalibration" name="InternalCalibration" version="2.0.0">
3 <description>Applies an internal calibration.</description>
4 <macros>
5 <token name="@EXECUTABLE@">InternalCalibration</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>InternalCalibration
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_ref_peaks:
19 -ref_peaks $param_ref_peaks
20 #end if
21 #if $param_type:
22 -type
23 #if " " in str($param_type):
24 "$param_type"
25 #else
26 $param_type
27 #end if
28 #end if
29 #if $param_trafo:
30 -trafo $param_trafo
31 #end if
32 -threads \${GALAXY_SLOTS:-24}
33 #if $param_algorithm_mz_tolerance:
34 -algorithm:mz_tolerance $param_algorithm_mz_tolerance
35 #end if
36 #if $param_algorithm_mz_tolerance_unit:
37 -algorithm:mz_tolerance_unit
38 #if " " in str($param_algorithm_mz_tolerance_unit):
39 "$param_algorithm_mz_tolerance_unit"
40 #else
41 $param_algorithm_mz_tolerance_unit
42 #end if
43 #end if
44 #if $param_algorithm_rt_tolerance:
45 -algorithm:rt_tolerance $param_algorithm_rt_tolerance
46 #end if
47 #if $adv_opts.adv_opts_selector=='advanced':
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #end if
52 </command>
53 <inputs>
54 <param name="param_in" type="data" format="featurexml,mzml" optional="False" label="input peak file" help="(-in) "/>
55 <param name="param_ref_peaks" type="data" format="tabular,idxml" optional="True" label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" help="(-ref_peaks) "/>
56 <param name="param_type" type="select" optional="True" value="spectrumwise" label="The kind of internal calibration that should be applied" help="(-type) ">
57 <option value="spectrumwise">spectrumwise</option>
58 <option value="global">global</option>
59 </param>
60 <param name="param_algorithm_mz_tolerance" type="float" min="0.0" optional="True" value="1.0" label="Allowed tolerance between peak and reference m/z" help="(-mz_tolerance) "/>
61 <param name="param_algorithm_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance" help="(-mz_tolerance_unit) ">
62 <option value="Da">Da</option>
63 <option value="ppm">ppm</option>
64 </param>
65 <param name="param_algorithm_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt" help="(-rt_tolerance) "/>
66 <expand macro="advanced_options">
67 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
68 </expand>
69 </inputs>
70 <outputs>
71 <data name="param_out" metadata_source="param_in" format="input"/>
72 <data name="param_trafo" format="trafoxml"/>
73 </outputs>
74 <help>**What it does**
75
76 Applies an internal calibration.
77
78
79 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
80 <expand macro="references"/>
81 </tool>