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comparison ERPairFinder.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="ERPairFinder" name="ERPairFinder" 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>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="ERPairFinder" name="ERPairFinder" version="2.0.0">
5 <token name="@EXECUTABLE@">ERPairFinder</token> 5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">ERPairFinder</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>ERPairFinder 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ERPairFinder
11 14
12 -in ${param_in} 15 #if $param_in:
13 -pair_in ${param_pair_in} 16 -in $param_in
14 -out ${param_out} 17 #end if
15 -feature_out ${param_feature_out} 18 #if $param_pair_in:
16 -precursor_mass_tolerance ${param_precursor_mass_tolerance} 19 -pair_in $param_pair_in
17 -threads \${GALAXY_SLOTS:-24} 20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_feature_out:
25 -feature_out $param_feature_out
26 #end if
27 #if $param_precursor_mass_tolerance:
28 -precursor_mass_tolerance $param_precursor_mass_tolerance
29 #end if
30 -threads \${GALAXY_SLOTS:-24}
18 #if $adv_opts.adv_opts_selector=='advanced': 31 #if $adv_opts.adv_opts_selector=='advanced':
19 -RT_tolerance ${adv_opts.param_RT_tolerance} 32 #if $adv_opts.param_RT_tolerance:
20 -max_charge ${adv_opts.param_max_charge} 33 -RT_tolerance $adv_opts.param_RT_tolerance
21 -intensity_threshold ${adv_opts.param_intensity_threshold} 34 #end if
22 -max_isotope ${adv_opts.param_max_isotope} 35 #if $adv_opts.param_max_charge:
23 -expansion_range ${adv_opts.param_expansion_range} 36 -max_charge $adv_opts.param_max_charge
37 #end if
38 #if $adv_opts.param_intensity_threshold:
39 -intensity_threshold $adv_opts.param_intensity_threshold
40 #end if
41 #if $adv_opts.param_max_isotope:
42 -max_isotope $adv_opts.param_max_isotope
43 #end if
44 #if $adv_opts.param_expansion_range:
45 -expansion_range $adv_opts.param_expansion_range
46 #end if
47 #if $adv_opts.param_force:
48 -force
49 #end if
24 #end if 50 #end if
25 </command> 51 </command>
26 <inputs> 52 <inputs>
27 <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file containing the ER spectra." help="(-in)"/> 53 <param format="mzml" help="(-in) " label="Input mzML file containing the ER spectra" name="param_in" optional="False" type="data"/>
28 <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in)"/> 54 <param format="txt" help="(-pair_in) " label="Pair-file in the format: m/z-light m/z-heavy charge rt" name="param_pair_in" optional="False" type="data"/>
29 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features." help="(-precursor_mass_tolerance)"/> 55 <param help="(-precursor_mass_tolerance) " label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" min="0.0" name="param_precursor_mass_tolerance" optional="True" type="float" value="0.3"/>
30 <expand macro="advanced_options"> 56 <expand macro="advanced_options">
31 <param name="param_RT_tolerance" type="float" min="1.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help="(-RT_tolerance)"/> 57 <param help="(-RT_tolerance) " label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" min="1.0" name="param_RT_tolerance" optional="True" type="float" value="200.0"/>
32 <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search for." help="(-max_charge)"/> 58 <param help="(-max_charge) " label="Maximal charge state features should be search fo" min="1" name="param_max_charge" optional="True" type="integer" value="3"/>
33 <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation." help="(-intensity_threshold)"/> 59 <param help="(-intensity_threshold) " label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" min="-1.0" name="param_intensity_threshold" optional="True" type="float" value="-1.0"/>
34 <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope)"/> 60 <param help="(-max_isotope) " label="Max isotope of the isotope distribution to be considered" min="2" name="param_max_isotope" optional="True" type="integer" value="3"/>
35 <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th." help="(-expansion_range)"/> 61 <param help="(-expansion_range) " label="The range that is used to extend the isotope distribution with null intensity peaks in Th" min="0.0" name="param_expansion_range" optional="True" type="float" value="5.0"/>
36 </expand> 62 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
37 </inputs> 63 </expand>
38 <outputs> 64 </inputs>
39 <data name="param_out" label="Output consensusXML file were the pairs of the feature are written into." format="consensusXML"/> 65 <outputs>
40 <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/> 66 <data format="consensusxml" name="param_out"/>
41 </outputs> 67 <data format="xml" name="param_feature_out"/>
42 <help>**What it does** 68 </outputs>
43 69 <help>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
44 Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
45 70
46 71
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html 72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html</help>
48 73 </tool>
49 @REFERENCES@
50 </help>
51 </tool>