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comparison FeatureFinderMRM.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
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="FeatureFinderMRM" name="FeatureFinderMRM" 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>Detects two-dimensional features in LC-MS data.</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="2.0.0">
5 <token name="@EXECUTABLE@">FeatureFinderMRM</token> 5 <description>Detects two-dimensional features in LC-MS data.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FeatureFinderMRM</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FeatureFinderMRM 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureFinderMRM
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -threads \${GALAXY_SLOTS:-24} 17 #end if
15 -algorithm:min_rt_distance ${param_min_rt_distance} 18 #if $param_out:
16 -algorithm:min_signal_to_noise_ratio ${param_min_signal_to_noise_ratio} 19 -out $param_out
20 #end if
21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_min_rt_distance:
23 -algorithm:min_rt_distance $param_algorithm_min_rt_distance
24 #end if
25 #if $param_algorithm_min_signal_to_noise_ratio:
26 -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
27 #end if
17 #if $adv_opts.adv_opts_selector=='advanced': 28 #if $adv_opts.adv_opts_selector=='advanced':
18 -algorithm:min_num_peaks_per_feature ${adv_opts.param_min_num_peaks_per_feature} 29 #if $adv_opts.param_force:
19 ${adv_opts.param_write_debug_files} 30 -force
20 ${adv_opts.param_resample_traces} 31 #end if
21 ${adv_opts.param_write_debuginfo} 32 #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
33 -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
34 #end if
35 #if $adv_opts.param_algorithm_write_debug_files:
36 -algorithm:write_debug_files
37 #end if
38 #if $adv_opts.param_algorithm_resample_traces:
39 -algorithm:resample_traces
40 #end if
41 #if $adv_opts.param_algorithm_write_debuginfo:
42 -algorithm:write_debuginfo
43 #end if
22 #end if 44 #end if
23 </command> 45 </command>
24 <inputs> 46 <inputs>
25 <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/> 47 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
26 <param name="param_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds." help="(-min_rt_distance)"/> 48 <param help="(-min_rt_distance) " label="Minimal distance of MRM features in seconds" min="0.0" name="param_algorithm_min_rt_distance" optional="True" type="float" value="10.0"/>
27 <param name="param_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise." help="(-min_signal_to_noise_ratio)"/> 49 <param help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise" label="Minimal S/N ratio a peak must have to be taken into account" min="0.0" name="param_algorithm_min_signal_to_noise_ratio" optional="True" type="float" value="2.0"/>
28 <expand macro="advanced_options"> 50 <expand macro="advanced_options">
29 <param name="param_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature)"/> 51 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
30 <param name="param_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files true" falsevalue="-algorithm:write_debug_files false" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files)"/> 52 <param help="(-min_num_peaks_per_feature) " label="Minimal number of peaks which are needed for a single feature" min="1" name="param_algorithm_min_num_peaks_per_feature" optional="True" type="integer" value="5"/>
31 <param name="param_resample_traces" type="boolean" truevalue="-algorithm:resample_traces true" falsevalue="-algorithm:resample_traces false" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces)"/> 53 <param checked="false" falsevalue="" help="(-write_debug_files) " label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" name="param_algorithm_write_debug_files" optional="True" truevalue="-algorithm:write_debug_files" type="boolean"/>
32 <param name="param_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo true" falsevalue="-algorithm:write_debuginfo false" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy." help="(-write_debuginfo)"/> 54 <param checked="false" falsevalue="" help="(-resample_traces) " label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" name="param_algorithm_resample_traces" optional="True" truevalue="-algorithm:resample_traces" type="boolean"/>
33 </expand> 55 <param checked="false" falsevalue="" help="(-write_debuginfo) " label="If set to true, debug messages are written, the output can be somewhat lengthy" name="param_algorithm_write_debuginfo" optional="True" truevalue="-algorithm:write_debuginfo" type="boolean"/>
34 </inputs> 56 </expand>
35 <outputs> 57 </inputs>
36 <data name="param_out" label="output file" format="featureXML"/> 58 <outputs>
37 </outputs> 59 <data format="xml" name="param_out"/>
38 <help>**What it does** 60 </outputs>
39 61 <help>Detects two-dimensional features in LC-MS data.
40 Detects two-dimensional features in LC-MS data.
41 62
42 63
43 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html 64 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html</help>
44 65 </tool>
45 @REFERENCES@
46 </help>
47 </tool>