Mercurial > repos > bgruening > openms

comparison InternalCalibration.xml @ 4:6ead64a594bd draft default tip

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