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comparison FeatureLinkerUnlabeledQT.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="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" 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>Groups corresponding features from multiple maps.</description> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <macros> 4 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="2.0.0">
5 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token> 5 <description>Groups corresponding features from multiple maps.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FeatureLinkerUnlabeledQT 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureLinkerUnlabeledQT
11 14
12 -in ${param_in} 15 -in
13 -out ${param_out} 16 #for token in $param_in:
14 ${param_keep_subelements} 17 $token
15 -threads \${GALAXY_SLOTS:-24} 18 #end for
16 ${param_use_identifications} 19 #if $param_out:
17 ${param_ignore_charge} 20 -out $param_out
18 -algorithm:distance_RT:max_difference ${param_max_difference} 21 #end if
19 -algorithm:distance_MZ:max_difference ${param_max_difference} 22 #if $param_keep_subelements:
20 -algorithm:distance_MZ:unit ${param_unit} 23 -keep_subelements
24 #end if
25 -threads \${GALAXY_SLOTS:-24}
26 #if $param_algorithm_use_identifications:
27 -algorithm:use_identifications
28 #end if
29 #if $param_algorithm_ignore_charge:
30 -algorithm:ignore_charge
31 #end if
32 #if $param_algorithm_distance_RT_max_difference:
33 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
34 #end if
35 #if $param_algorithm_distance_MZ_max_difference:
36 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
37 #end if
38 #if $param_algorithm_distance_MZ_unit:
39 -algorithm:distance_MZ:unit
40 #if &quot; &quot; in str($param_algorithm_distance_MZ_unit):
41 &quot;$param_algorithm_distance_MZ_unit&quot;
42 #else
43 $param_algorithm_distance_MZ_unit
44 #end if
45 #end if
21 #if $adv_opts.adv_opts_selector=='advanced': 46 #if $adv_opts.adv_opts_selector=='advanced':
22 -algorithm:distance_RT:exponent ${adv_opts.param_exponent} 47 #if $adv_opts.param_force:
23 -algorithm:distance_RT:weight ${adv_opts.param_weight} 48 -force
24 -algorithm:distance_MZ:exponent ${adv_opts.param_exponent} 49 #end if
25 -algorithm:distance_MZ:weight ${adv_opts.param_weight} 50 #if $adv_opts.param_algorithm_distance_RT_exponent:
26 -algorithm:distance_intensity:exponent ${adv_opts.param_exponent} 51 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
27 -algorithm:distance_intensity:weight ${adv_opts.param_weight} 52 #end if
53 #if $adv_opts.param_algorithm_distance_RT_weight:
54 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
55 #end if
56 #if $adv_opts.param_algorithm_distance_MZ_exponent:
57 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
58 #end if
59 #if $adv_opts.param_algorithm_distance_MZ_weight:
60 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
61 #end if
62 #if $adv_opts.param_algorithm_distance_intensity_exponent:
63 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
64 #end if
65 #if $adv_opts.param_algorithm_distance_intensity_weight:
66 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
67 #end if
28 #end if 68 #end if
29 </command> 69 </command>
30 <inputs> 70 <inputs>
31 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/> 71 <param format="xml,consensusxml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
32 <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)"/> 72 <sanitizer>
33 <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)"/> 73 <valid initial="string.printable">
34 <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)"/> 74 <remove value="'"/>
35 <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)"/> 75 <remove value="&quot;"/>
36 <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)"/> 76 </valid>
37 <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)"> 77 </sanitizer>
38 <option value="Da">Da</option> 78 </param>
39 <option value="ppm">ppm</option> 79 <param checked="false" falsevalue="" help="(-keep_subelements) " label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" name="param_keep_subelements" optional="True" truevalue="-keep_subelements" type="boolean"/>
40 </param> 80 <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" name="param_algorithm_use_identifications" optional="True" truevalue="-algorithm:use_identifications" type="boolean"/>
41 <expand macro="advanced_options"> 81 <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_ignore_charge" optional="True" truevalue="-algorithm:ignore_charge" type="boolean"/>
42 <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)"/> 82 <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_distance_RT_max_difference" optional="True" type="float" value="100.0"/>
43 <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/> 83 <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_distance_MZ_max_difference" optional="True" type="float" value="0.3"/>
44 <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)"/> 84 <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_distance_MZ_unit" optional="True" type="select" value="Da">
45 <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)"/> 85 <option value="Da">Da</option>
46 <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)"/> 86 <option value="ppm">ppm</option>
47 <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)"/> 87 </param>
48 </expand> 88 <expand macro="advanced_options">
49 </inputs> 89 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
50 <outputs> 90 <param help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_RT_exponent" optional="True" type="float" value="1.0"/>
51 <data name="param_out" label="Output file" format="consensusXML"/> 91 <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_distance_RT_weight" optional="True" type="float" value="1.0"/>
52 </outputs> 92 <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_MZ_exponent" optional="True" type="float" value="2.0"/>
53 <help>**What it does** 93 <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_distance_MZ_weight" optional="True" type="float" value="1.0"/>
54 94 <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_intensity_exponent" optional="True" type="float" value="1.0"/>
55 Groups corresponding features from multiple maps. 95 <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_distance_intensity_weight" optional="True" type="float" value="0.0"/>
96 </expand>
97 </inputs>
98 <outputs>
99 <data format="consensusxml" name="param_out"/>
100 </outputs>
101 <help>Groups corresponding features from multiple maps.
56 102
57 103
58 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledQT.html 104 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledQT.html</help>
59 105 </tool>
60 @REFERENCES@
61 </help>
62 </tool>