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comparison OpenSwathChromatogramExtractor.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.0.0">
3 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathChromatogramExtractor
11
12 -in
13 #for token in $param_in:
14 $token
15 #end for
16 #if $param_tr:
17 -tr $param_tr
18 #end if
19 #if $param_rt_norm:
20 -rt_norm $param_rt_norm
21 #end if
22 #if $param_out:
23 -out $param_out
24 #end if
25 #if $param_min_upper_edge_dist:
26 -min_upper_edge_dist $param_min_upper_edge_dist
27 #end if
28 #if $param_mz_window:
29 -mz_window $param_mz_window
30 #end if
31 #if $param_rt_window:
32 -rt_window $param_rt_window
33 #end if
34 #if $param_is_swath:
35 -is_swath
36 #end if
37 #if $param_ppm:
38 -ppm
39 #end if
40 #if $param_extract_MS1:
41 -extract_MS1
42 #end if
43 #if $param_extraction_function:
44 -extraction_function
45 #if " " in str($param_extraction_function):
46 "$param_extraction_function"
47 #else
48 $param_extraction_function
49 #end if
50 #end if
51 -threads \${GALAXY_SLOTS:-24}
52 #if $param_model_type:
53 -model:type
54 #if " " in str($param_model_type):
55 "$param_model_type"
56 #else
57 $param_model_type
58 #end if
59 #end if
60 #if $param_model_symmetric_regression:
61 -model:symmetric_regression
62 #end if
63 #if $adv_opts.adv_opts_selector=='advanced':
64 #if $adv_opts.param_force:
65 -force
66 #end if
67 #end if
68 </command>
69 <inputs>
70 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
71 <sanitizer>
72 <valid initial="string.printable">
73 <remove value="'"/>
74 <remove value="&quot;"/>
75 </valid>
76 </sanitizer>
77 </param>
78 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
79 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
80 <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" help="(-min_upper_edge_dist) "/>
81 <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side"/>
82 <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
83 <param name="param_is_swath" type="boolean" truevalue="-is_swath" falsevalue="" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath) "/>
84 <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
85 <param name="param_extract_MS1" type="boolean" truevalue="-extract_MS1" falsevalue="" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1) "/>
86 <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
87 <option value="tophat">tophat</option>
88 <option value="bartlett">bartlett</option>
89 </param>
90 <param name="param_model_type" type="select" optional="True" value="linear" label="Type of model" help="(-type) ">
91 <option value="linear">linear</option>
92 <option value="b_spline">b_spline</option>
93 <option value="interpolated">interpolated</option>
94 </param>
95 <param name="param_model_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
96 <expand macro="advanced_options">
97 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
98 </expand>
99 </inputs>
100 <outputs>
101 <data name="param_out" format="mzml"/>
102 </outputs>
103 <help>**What it does**
104
105 Extract chromatograms (XIC) from a MS2 map file.
106
107
108 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html</help>
109 <expand macro="references"/>
110 </tool>