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comparison SpectraFilterBernNorm.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
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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="SpectraFilterBernNorm" name="SpectraFilterBernNorm" 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>Applies thresholdfilter to peak spectra.</description> 3 <!--Proposed Tool Section: [Identification]-->
4 <macros> 4 <tool id="SpectraFilterBernNorm" name="SpectraFilterBernNorm" version="2.0.0">
5 <token name="@EXECUTABLE@">SpectraFilterBernNorm</token> 5 <description>Applies thresholdfilter to peak spectra.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SpectraFilterBernNorm</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SpectraFilterBernNorm 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraFilterBernNorm
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:threshold ${param_threshold} 18 #if $param_out:
19 -out $param_out
20 #end if
21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_threshold:
23 -algorithm:threshold $param_algorithm_threshold
24 #end if
16 #if $adv_opts.adv_opts_selector=='advanced': 25 #if $adv_opts.adv_opts_selector=='advanced':
17 -algorithm:C1 ${adv_opts.param_C1} 26 #if $adv_opts.param_force:
18 -algorithm:C2 ${adv_opts.param_C2} 27 -force
28 #end if
29 #if $adv_opts.param_algorithm_C1:
30 -algorithm:C1 $adv_opts.param_algorithm_C1
31 #end if
32 #if $adv_opts.param_algorithm_C2:
33 -algorithm:C2 $adv_opts.param_algorithm_C2
34 #end if
19 #end if 35 #end if
20 </command> 36 </command>
21 <inputs> 37 <inputs>
22 <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/> 38 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
23 <param name="param_threshold" type="float" value="0.1" label="Threshold of the Bern et al. normalization." help="(-threshold)"/> 39 <param help="(-threshold) " label="Threshold of the Bern et al. normalization" name="param_algorithm_threshold" type="float" value="0.1"/>
24 <expand macro="advanced_options"> 40 <expand macro="advanced_options">
25 <param name="param_C1" type="float" value="28.0" label="C1 value of the normalization." help="(-C1)"/> 41 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
26 <param name="param_C2" type="float" value="400.0" label="C2 value of the normalization." help="(-C2)"/> 42 <param help="(-C1) " label="C1 value of the normalization" name="param_algorithm_C1" type="float" value="28.0"/>
27 </expand> 43 <param help="(-C2) " label="C2 value of the normalization" name="param_algorithm_C2" type="float" value="400.0"/>
28 </inputs> 44 </expand>
29 <outputs> 45 </inputs>
30 <data name="param_out" label="output file " format="mzML"/> 46 <outputs>
31 </outputs> 47 <data format="mzml" name="param_out"/>
32 <help>**What it does** 48 </outputs>
33 49 <help>Applies thresholdfilter to peak spectra.
34 Applies thresholdfilter to peak spectra.
35 50
36 51
37 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterBernNorm.html 52 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterBernNorm.html</help>
38 53 </tool>
39 @REFERENCES@
40 </help>
41 </tool>