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comparison FeatureLinkerLabeled.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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" 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 isotope-labeled features in a feature map.</description> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <macros> 4 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.0.0">
5 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token> 5 <description>Groups corresponding isotope-labeled features in a feature map.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FeatureLinkerLabeled 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureLinkerLabeled
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 ${param_rt_estimate} 18 #if $param_out:
16 -algorithm:rt_pair_dist ${param_rt_pair_dist} 19 -out $param_out
17 -algorithm:rt_dev_low ${param_rt_dev_low} 20 #end if
18 -algorithm:rt_dev_high ${param_rt_dev_high} 21 -threads \${GALAXY_SLOTS:-24}
19 -algorithm:mz_pair_dists ${param_mz_pair_dists} 22 #if $param_algorithm_rt_estimate:
20 -algorithm:mz_dev ${param_mz_dev} 23 -algorithm:rt_estimate
24 #end if
25 #if $param_algorithm_rt_pair_dist:
26 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
27 #end if
28 #if $param_algorithm_rt_dev_low:
29 -algorithm:rt_dev_low $param_algorithm_rt_dev_low
30 #end if
31 #if $param_algorithm_rt_dev_high:
32 -algorithm:rt_dev_high $param_algorithm_rt_dev_high
33 #end if
34
35 #if $rep_param_algorithm_mz_pair_dists:
36 -algorithm:mz_pair_dists
37 #for token in $rep_param_algorithm_mz_pair_dists:
38 #if &quot; &quot; in str(token):
39 &quot;$token.param_algorithm_mz_pair_dists&quot;
40 #else
41 $token.param_algorithm_mz_pair_dists
42 #end if
43 #end for
44 #end if
45 #if $param_algorithm_mz_dev:
46 -algorithm:mz_dev $param_algorithm_mz_dev
47 #end if
21 #if $adv_opts.adv_opts_selector=='advanced': 48 #if $adv_opts.adv_opts_selector=='advanced':
22 ${adv_opts.param_mrm} 49 #if $adv_opts.param_force:
50 -force
51 #end if
52 #if $adv_opts.param_algorithm_mrm:
53 -algorithm:mrm
54 #end if
23 #end if 55 #end if
24 </command> 56 </command>
25 <inputs> 57 <inputs>
26 <param name="param_in" type="data" format="featureXML" optional="False" label="Input file" help="(-in)"/> 58 <param format="xml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
27 <param name="param_rt_estimate" type="boolean" truevalue="-algorithm:rt_estimate true" falsevalue="-algorithm:rt_estimate false" checked="true" optional="True" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance." help="(-rt_estimate)"/> 59 <param checked="true" falsevalue="" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" name="param_algorithm_rt_estimate" optional="True" truevalue="-algorithm:rt_estimate" type="boolean"/>
28 <param name="param_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist)"/> 60 <param help="(-rt_pair_dist) " label="optimal pair distance in RT [sec] from light to heavy feature" name="param_algorithm_rt_pair_dist" type="float" value="-20.0"/>
29 <param name="param_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low)"/> 61 <param help="(-rt_dev_low) " label="maximum allowed deviation below optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_low" optional="True" type="float" value="15.0"/>
30 <param name="param_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high)"/> 62 <param help="(-rt_dev_high) " label="maximum allowed deviation above optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_high" optional="True" type="float" value="15.0"/>
31 <param name="param_mz_pair_dists" type="text" size="20" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)" help="(-mz_pair_dists)"/> 63 <repeat max="1" min="0" name="rep_param_algorithm_mz_pair_dists" title="param_algorithm_mz_pair_dists">
32 <param name="param_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance#br#" help="(-mz_dev)"/> 64 <param help="(-mz_pair_dists) by division through charge)" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." name="param_algorithm_mz_pair_dists" size="30" type="text" value="4.0">
33 <expand macro="advanced_options"> 65 <sanitizer>
34 <param name="param_mrm" type="boolean" truevalue="-algorithm:mrm true" falsevalue="-algorithm:mrm false" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm)"/> 66 <valid initial="string.printable">
35 </expand> 67 <remove value="'"/>
36 </inputs> 68 <remove value="&quot;"/>
37 <outputs> 69 </valid>
38 <data name="param_out" label="Output file" format="consensusXML"/> 70 </sanitizer>
39 </outputs> 71 </param>
40 <help>**What it does** 72 </repeat>
41 73 <param help="(-mz_dev) " label="maximum allowed deviation from optimal m/z distance" min="0.0" name="param_algorithm_mz_dev" optional="True" type="float" value="0.05"/>
42 Groups corresponding isotope-labeled features in a feature map. 74 <expand macro="advanced_options">
75 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
76 <param checked="false" falsevalue="" help="(-mrm) " label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" name="param_algorithm_mrm" optional="True" truevalue="-algorithm:mrm" type="boolean"/>
77 </expand>
78 </inputs>
79 <outputs>
80 <data format="consensusxml" name="param_out"/>
81 </outputs>
82 <help>Groups corresponding isotope-labeled features in a feature map.
43 83
44 84
45 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html 85 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help>
46 86 </tool>
47 @REFERENCES@
48 </help>
49 </tool>