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comparison SpectraFilterWindowMower.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="SpectraFilterWindowMower" name="SpectraFilterWindowMower" 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="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="2.0.0">
5 <token name="@EXECUTABLE@">SpectraFilterWindowMower</token> 5 <description>Applies thresholdfilter to peak spectra.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SpectraFilterWindowMower</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SpectraFilterWindowMower 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraFilterWindowMower
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:windowsize ${param_windowsize} 18 #if $param_out:
16 -algorithm:peakcount ${param_peakcount} 19 -out $param_out
17 -algorithm:movetype ${param_movetype} 20 #end if
21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_windowsize:
23 -algorithm:windowsize $param_algorithm_windowsize
24 #end if
25 #if $param_algorithm_peakcount:
26 -algorithm:peakcount $param_algorithm_peakcount
27 #end if
28 #if $param_algorithm_movetype:
29 -algorithm:movetype
30 #if &quot; &quot; in str($param_algorithm_movetype):
31 &quot;$param_algorithm_movetype&quot;
32 #else
33 $param_algorithm_movetype
34 #end if
35 #end if
36 #if $adv_opts.adv_opts_selector=='advanced':
37 #if $adv_opts.param_force:
38 -force
39 #end if
40 #end if
18 </command> 41 </command>
19 <inputs> 42 <inputs>
20 <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/> 43 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
21 <param name="param_windowsize" type="float" value="50.0" label="The size of the sliding window along the m/z axis." help="(-windowsize)"/> 44 <param help="(-windowsize) " label="The size of the sliding window along the m/z axis" name="param_algorithm_windowsize" type="float" value="50.0"/>
22 <param name="param_peakcount" type="integer" value="2" label="The number of peaks that should be kept." help="(-peakcount)"/> 45 <param help="(-peakcount) " label="The number of peaks that should be kept" name="param_algorithm_peakcount" type="integer" value="2"/>
23 <param name="param_movetype" type="select" optional="True" value="slide" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used." help="(-movetype)"> 46 <param help="(-movetype) " label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" name="param_algorithm_movetype" optional="True" type="select" value="slide">
24 <option value="slide">slide</option> 47 <option value="slide">slide</option>
25 <option value="jump">jump</option> 48 <option value="jump">jump</option>
26 </param> 49 </param>
27 </inputs> 50 <expand macro="advanced_options">
28 <outputs> 51 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
29 <data name="param_out" label="output file " format="mzML"/> 52 </expand>
30 </outputs> 53 </inputs>
31 <help>**What it does** 54 <outputs>
32 55 <data format="mzml" name="param_out"/>
33 Applies thresholdfilter to peak spectra. 56 </outputs>
57 <help>Applies thresholdfilter to peak spectra.
34 58
35 59
36 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html 60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html</help>
37 61 </tool>
38 @REFERENCES@
39 </help>
40 </tool>