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comparison EICExtractor.xml @ 0:0cdc3e405e3c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:20:46 -0500
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children d5d9063b9cfc
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-1:000000000000 0:0cdc3e405e3c
1 <?xml version='1.0' encoding='UTF-8'?>
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 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="EICExtractor" name="EICExtractor" version="2.1.0">
5 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
6 <macros>
7 <token name="@EXECUTABLE@">EICExtractor</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>EICExtractor
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 -in_header
20 #for token in $param_in_header:
21 $token
22 #end for
23 #if $param_pos:
24 -pos $param_pos
25 #end if
26 #if $param_rt_tol:
27 -rt_tol $param_rt_tol
28 #end if
29 #if $param_mz_tol:
30 -mz_tol $param_mz_tol
31 #end if
32 #if $param_rt_collect:
33 -rt_collect $param_rt_collect
34 #end if
35 #if $param_out:
36 -out $param_out
37 #end if
38 #if $param_auto_rt_enabled:
39 -auto_rt:enabled
40 #end if
41 #if $param_auto_rt_out_debug_TIC:
42 -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
43 #end if
44 #if $adv_opts.adv_opts_selector=='advanced':
45 #if $adv_opts.param_out_separator:
46 -out_separator "$adv_opts.param_out_separator"
47 #end if
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #if $adv_opts.param_auto_rt_FHWM:
52 -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
53 #end if
54 #if $adv_opts.param_auto_rt_SNThreshold:
55 -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
56 #end if
57 #end if
58 </command>
59 <inputs>
60 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input raw data file" help="(-in) ">
61 <sanitizer>
62 <valid initial="string.printable">
63 <remove value="'"/>
64 <remove value="&quot;"/>
65 </valid>
66 </sanitizer>
67 </param>
68 <param name="param_in_header" type="data" format="txt" multiple="true" optional="True" size="30" label="[for Waters data only] Read additional information from _HEADER.TXT" help="(-in_header) Provide one for each raw input file">
69 <sanitizer>
70 <valid initial="string.printable">
71 <remove value="'"/>
72 <remove value="&quot;"/>
73 </valid>
74 </sanitizer>
75 </param>
76 <param name="param_pos" type="data" format="tabular" optional="False" label="Input config file stating where to find signal" help="(-pos) "/>
77 <param name="param_rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
78 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
79 <param name="param_rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help="(-rt_collect) "/>
80 <param name="param_auto_rt_enabled" display="radio" type="boolean" truevalue="-auto_rt:enabled" falsevalue="" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help="(-enabled) "/>
81 <expand macro="advanced_options">
82 <param name="param_out_separator" type="text" size="30" value="," label="Separator character for output CSV file" help="(-out_separator) ">
83 <sanitizer>
84 <valid initial="string.printable">
85 <remove value="'"/>
86 <remove value="&quot;"/>
87 </valid>
88 </sanitizer>
89 </param>
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
91 <param name="param_auto_rt_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC"/>
92 <param name="param_auto_rt_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="(-SNThreshold) Higher thesholds will result in less peaks"/>
93 </expand>
94 </inputs>
95 <outputs>
96 <data name="param_out" format="tabular"/>
97 <data name="param_auto_rt_out_debug_TIC" format="mzml"/>
98 </outputs>
99 <help>Extracts intensities from dedicates positions in a LC/MS map
100
101
102 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html</help>
103 </tool>