Mercurial > repos > bgruening > openms

annotate SpectraFilterWindowMower.xml @ 4:6ead64a594bd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
3 <!--Proposed Tool Section: [Identification]-->
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
4 <tool id="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="2.0.0">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
5 <description>Applies thresholdfilter to peak spectra.</description>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
6 <macros>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
7 <token name="@EXECUTABLE@">SpectraFilterWindowMower</token>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
8 <import>macros.xml</import>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
9 </macros>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
10 <expand macro="references"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
11 <expand macro="stdio"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
12 <expand macro="requirements"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
13 <command>SpectraFilterWindowMower
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
14
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
15 #if $param_in:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
16 -in $param_in
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
17 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
18 #if $param_out:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
19 -out $param_out
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
20 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
21 -threads \${GALAXY_SLOTS:-24}
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
22 #if $param_algorithm_windowsize:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
23 -algorithm:windowsize $param_algorithm_windowsize
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
24 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
25 #if $param_algorithm_peakcount:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
26 -algorithm:peakcount $param_algorithm_peakcount
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
27 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
28 #if $param_algorithm_movetype:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
29 -algorithm:movetype
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
30 #if &quot; &quot; in str($param_algorithm_movetype):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
31 &quot;$param_algorithm_movetype&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
32 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
33 $param_algorithm_movetype
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
34 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
35 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
36 #if $adv_opts.adv_opts_selector=='advanced':
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
37 #if $adv_opts.param_force:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
38 -force
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
39 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
40 #end if
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
41 </command>
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
42 <inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
43 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
45 <param help="(-peakcount) " label="The number of peaks that should be kept" name="param_algorithm_peakcount" type="integer" value="2"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
47 <option value="slide">slide</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
48 <option value="jump">jump</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
49 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
50 <expand macro="advanced_options">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
51 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
52 </expand>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
53 </inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
54 <outputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
55 <data format="mzml" name="param_out"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
56 </outputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
57 <help>Applies thresholdfilter to peak spectra.
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
58
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
59
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html</help>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
61 </tool>