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comparison FeatureLinkerUnlabeled.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="1.12.0">
3 <description>Groups corresponding features from multiple maps.</description>
4 <macros>
5 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>FeatureLinkerUnlabeled
11
12 -in ${param_in}
13 -out ${param_out}
14 ${param_keep_subelements}
15 -threads \${GALAXY_SLOTS:-24}
16 -algorithm:second_nearest_gap ${param_second_nearest_gap}
17 ${param_use_identifications}
18 ${param_ignore_charge}
19 -algorithm:distance_RT:max_difference ${param_max_difference}
20 -algorithm:distance_MZ:max_difference ${param_max_difference}
21 -algorithm:distance_MZ:unit ${param_unit}
22 #if $adv_opts.adv_opts_selector=='advanced':
23 -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
24 -algorithm:distance_RT:weight ${adv_opts.param_weight}
25 -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
26 -algorithm:distance_MZ:weight ${adv_opts.param_weight}
27 -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
28 -algorithm:distance_intensity:weight ${adv_opts.param_weight}
29 #end if
30 </command>
31 <inputs>
32 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
33 <param name="param_keep_subelements" type="boolean" truevalue="-keep_subelements true" falsevalue="-keep_subelements false" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." help="(-keep_subelements)"/>
34 <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/>
35 <param name="param_use_identifications" type="boolean" truevalue="-algorithm:use_identifications true" falsevalue="-algorithm:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/>
36 <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge true" falsevalue="-algorithm:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/>
37 <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/>
38 <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/>
39 <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)">
40 <option value="Da">Da</option>
41 <option value="ppm">ppm</option>
42 </param>
43 <expand macro="advanced_options">
44 <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
45 <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/>
46 <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
47 <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/>
48 <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
49 <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/>
50 </expand>
51 </inputs>
52 <outputs>
53 <data name="param_out" label="Output file" format="consensusXML"/>
54 </outputs>
55 <help>**What it does**
56
57 Groups corresponding features from multiple maps.
58
59
60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html
61
62 @REFERENCES@
63 </help>
64 </tool>