Mercurial > repos > galaxyp > openms_openswathchromatogramextractor

comparison OpenSwathChromatogramExtractor.xml @ 0:f41f97505717 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 12:43:05 -0500
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children 47729465a3d3
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-1:000000000000 0:f41f97505717
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: [Targeted Experiments]-->
4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.1.0">
5 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathChromatogramExtractor
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_tr:
20 -tr $param_tr
21 #end if
22 #if $param_rt_norm:
23 -rt_norm $param_rt_norm
24 #end if
25 #if $param_out:
26 -out $param_out
27 #end if
28 #if $param_min_upper_edge_dist:
29 -min_upper_edge_dist $param_min_upper_edge_dist
30 #end if
31 #if $param_mz_window:
32 -mz_window $param_mz_window
33 #end if
34 #if $param_rt_window:
35 -rt_window $param_rt_window
36 #end if
37 #if $param_is_swath:
38 -is_swath
39 #end if
40 #if $param_ppm:
41 -ppm
42 #end if
43 #if $param_extract_MS1:
44 -extract_MS1
45 #end if
46 #if $param_extraction_function:
47 -extraction_function $param_extraction_function
48 #end if
49 #if $param_model_type:
50 -model:type $param_model_type
51 #end if
52 #if $param_model_symmetric_regression:
53 -model:symmetric_regression
54 #end if
55 #if $adv_opts.adv_opts_selector=='advanced':
56 #if $adv_opts.param_force:
57 -force
58 #end if
59 #end if
60 </command>
61 <inputs>
62 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
63 <sanitizer>
64 <valid initial="string.printable">
65 <remove value="'"/>
66 <remove value="&quot;"/>
67 </valid>
68 </sanitizer>
69 </param>
70 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
71 <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) "/>
72 <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) "/>
73 <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"/>
74 <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"/>
75 <param name="param_is_swath" display="radio" type="boolean" truevalue="-is_swath" falsevalue="" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath) "/>
76 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
77 <param name="param_extract_MS1" display="radio" 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) "/>
78 <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
79 <option value="tophat" selected="true">tophat</option>
80 <option value="bartlett">bartlett</option>
81 </param>
82 <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) ">
83 <option value="linear" selected="true">linear</option>
84 <option value="b_spline">b_spline</option>
85 <option value="interpolated">interpolated</option>
86 <option value="lowess">lowess</option>
87 </param>
88 <param name="param_model_symmetric_regression" display="radio" 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'"/>
89 <expand macro="advanced_options">
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
91 </expand>
92 </inputs>
93 <outputs>
94 <data name="param_out" format="mzml"/>
95 </outputs>
96 <help>Extract chromatograms (XIC) from a MS2 map file.
97
98
99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html</help>
100 </tool>