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comparison OpenSwathDIAPreScoring.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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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" 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>Scoring spectra using the DIA scores.</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token> 5 <description>Scoring spectra using the DIA scores.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathDIAPreScoring 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathDIAPreScoring
11 14
12 -tr ${param_tr} 15 #if $param_tr:
13 -out ${param_out} 16 -tr $param_tr
14 -swath_files ${param_swath_files} 17 #end if
15 -min_upper_edge_dist ${param_min_upper_edge_dist} 18 #if $param_out:
16 -threads \${GALAXY_SLOTS:-24} 19 -out $param_out
20 #end if
21 -swath_files
22 #for token in $param_swath_files:
23 $token
24 #end for
25 #if $param_min_upper_edge_dist:
26 -min_upper_edge_dist $param_min_upper_edge_dist
27 #end if
28 -threads \${GALAXY_SLOTS:-24}
29 #if $adv_opts.adv_opts_selector=='advanced':
30 #if $adv_opts.param_force:
31 -force
32 #end if
33 #end if
17 </command> 34 </command>
18 <inputs> 35 <inputs>
19 <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/> 36 <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/>
20 <param name="param_swath_files" type="data" format="mzML" optional="True" size="20" label="Swath files that were used to extract the transitions. If present, SWATH specific scoring will be applied." help="(-swath_files)"/> 37 <param format="mzml" help="(-swath_files) If present, SWATH specific scoring will be applied" label="Swath files that were used to extract the transitions" multiple="true" name="param_swath_files" optional="True" size="30" type="data">
21 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist)"/> 38 <sanitizer>
22 </inputs> 39 <valid initial="string.printable">
23 <outputs> 40 <remove value="'"/>
24 <data name="param_out" label="output file" format="data"/> 41 <remove value="&quot;"/>
25 </outputs> 42 </valid>
26 <help>**What it does** 43 </sanitizer>
27 44 </param>
28 Scoring spectra using the DIA scores. 45 <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" name="param_min_upper_edge_dist" type="float" value="0.0"/>
46 <expand macro="advanced_options">
47 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
48 </expand>
49 </inputs>
50 <outputs>
51 <data format="tabular" name="param_out"/>
52 </outputs>
53 <help>Scoring spectra using the DIA scores.
29 54
30 55
31 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html 56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html</help>
32 57 </tool>
33 @REFERENCES@
34 </help>
35 </tool>