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comparison OpenSwathChromatogramExtractor.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
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" 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>Extract chromatograms (XIC) from a MS2 map file.</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token> 5 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathChromatogramExtractor 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathChromatogramExtractor
11 14
12 -in ${param_in} 15 -in
13 -tr ${param_tr} 16 #for token in $param_in:
14 -rt_norm ${param_rt_norm} 17 $token
15 -out ${param_out} 18 #end for
16 -min_upper_edge_dist ${param_min_upper_edge_dist} 19 #if $param_tr:
17 -mz_window ${param_mz_window} 20 -tr $param_tr
18 -rt_window ${param_rt_window} 21 #end if
19 ${param_is_swath} 22 #if $param_rt_norm:
20 ${param_ppm} 23 -rt_norm $param_rt_norm
21 ${param_extract_MS1} 24 #end if
22 -extraction_function ${param_extraction_function} 25 #if $param_out:
23 -threads \${GALAXY_SLOTS:-24} 26 -out $param_out
24 -model:type ${param_type} 27 #end if
25 ${param_symmetric_regression} 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 $param_extraction_function:
47 -extraction_function
48 #if &quot; &quot; in str($param_extraction_function):
49 &quot;$param_extraction_function&quot;
50 #else
51 $param_extraction_function
52 #end if
53 #end if
54 -threads \${GALAXY_SLOTS:-24}
55 #if $param_model_type:
56 -model:type
57 #if &quot; &quot; in str($param_model_type):
58 &quot;$param_model_type&quot;
59 #else
60 $param_model_type
61 #end if
62 #end if
63 #if $param_model_symmetric_regression:
64 -model:symmetric_regression
65 #end if
66 #if $adv_opts.adv_opts_selector=='advanced':
67 #if $adv_opts.param_force:
68 -force
69 #end if
70 #end if
26 </command> 71 </command>
27 <inputs> 72 <inputs>
28 <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/> 73 <param format="mzml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
29 <param name="param_tr" type="data" format="tabular" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr)"/> 74 <sanitizer>
30 <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm)"/> 75 <valid initial="string.printable">
31 <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)"/> 76 <remove value="'"/>
32 <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, e.g. 100 ppm would extract 50 ppm on either side." help="(-mz_window)"/> 77 <remove value="&quot;"/>
33 <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, e.g. a value of 1000 seconds would extract 500 seconds on either side." help="(-rt_window)"/> 78 </valid>
34 <param name="param_is_swath" type="boolean" truevalue="-is_swath true" falsevalue="-is_swath false" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath)"/> 79 </sanitizer>
35 <param name="param_ppm" type="boolean" truevalue="-ppm true" falsevalue="-ppm false" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm)"/> 80 </param>
36 <param name="param_extract_MS1" type="boolean" truevalue="-extract_MS1 true" falsevalue="-extract_MS1 false" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1)"/> 81 <param format="tabular,traml" help="(-tr) " label="transition file ('TraML' or 'csv')" name="param_tr" optional="False" type="data"/>
37 <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function)"> 82 <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/>
38 <option value="tophat">tophat</option> 83 <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson" name="param_min_upper_edge_dist" type="float" value="0.0"/>
39 <option value="bartlett">bartlett</option> 84 <param help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," min="0.0" name="param_mz_window" optional="True" type="float" value="0.05"/>
40 </param> 85 <param help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," name="param_rt_window" type="float" value="-1.0"/>
41 <param name="param_type" type="select" optional="True" value="linear" label="Type of model" help="(-type)"> 86 <param checked="false" falsevalue="" help="(-is_swath) " label="Set this flag if the data is SWATH data" name="param_is_swath" optional="True" truevalue="-is_swath" type="boolean"/>
42 <option value="linear">linear</option> 87 <param checked="false" falsevalue="" help="(-ppm) " label="m/z extraction_window is in ppm" name="param_ppm" optional="True" truevalue="-ppm" type="boolean"/>
43 <option value="b_spline">b_spline</option> 88 <param checked="false" falsevalue="" help="(-extract_MS1) " label="Extract the MS1 transitions based on the precursor values in the TraML file" name="param_extract_MS1" optional="True" truevalue="-extract_MS1" type="boolean"/>
44 <option value="interpolated">interpolated</option> 89 <param help="(-extraction_function) " label="Function used to extract the signal" name="param_extraction_function" optional="True" type="select" value="tophat">
45 </param> 90 <option value="tophat">tophat</option>
46 <param name="param_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression true" falsevalue="-model:symmetric_regression false" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/> 91 <option value="bartlett">bartlett</option>
47 </inputs> 92 </param>
48 <outputs> 93 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="linear">
49 <data name="param_out" label="output file" format="mzML"/> 94 <option value="linear">linear</option>
50 </outputs> 95 <option value="b_spline">b_spline</option>
51 <help>**What it does** 96 <option value="interpolated">interpolated</option>
52 97 </param>
53 Extract chromatograms (XIC) from a MS2 map file. 98 <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" name="param_model_symmetric_regression" optional="True" truevalue="-model:symmetric_regression" type="boolean"/>
99 <expand macro="advanced_options">
100 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
101 </expand>
102 </inputs>
103 <outputs>
104 <data format="mzml" name="param_out"/>
105 </outputs>
106 <help>Extract chromatograms (XIC) from a MS2 map file.
54 107
55 108
56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html 109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html</help>
57 110 </tool>
58 @REFERENCES@
59 </help>
60 </tool>