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comparison EICExtractor.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="EICExtractor" name="EICExtractor" 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>Extracts intensities from dedicates positions in a LC/MS map</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="EICExtractor" name="EICExtractor" version="2.0.0">
5 <token name="@EXECUTABLE@">EICExtractor</token> 5 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">EICExtractor</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>EICExtractor 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>EICExtractor
11 14
12 -in ${param_in} 15 -in
13 -in_header ${param_in_header} 16 #for token in $param_in:
14 -pos ${param_pos} 17 $token
15 -rt_tol ${param_rt_tol} 18 #end for
16 -mz_tol ${param_mz_tol} 19 -in_header
17 -rt_collect ${param_rt_collect} 20 #for token in $param_in_header:
18 -out ${param_out} 21 $token
19 -threads \${GALAXY_SLOTS:-24} 22 #end for
20 ${param_enabled} 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 -threads \${GALAXY_SLOTS:-24}
39 #if $param_auto_rt_enabled:
40 -auto_rt:enabled
41 #end if
42 #if $param_auto_rt_out_debug_TIC:
43 -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
44 #end if
21 #if $adv_opts.adv_opts_selector=='advanced': 45 #if $adv_opts.adv_opts_selector=='advanced':
22 -out_separator ${adv_opts.param_out_separator} 46 #if $adv_opts.param_out_separator:
23 -auto_rt:FHWM ${adv_opts.param_FHWM} 47 -out_separator &quot;$adv_opts.param_out_separator&quot;
24 -auto_rt:SNThreshold ${adv_opts.param_SNThreshold} 48 #end if
25 -auto_rt:out_debug_TIC ${adv_opts.param_out_debug_TIC} 49 #if $adv_opts.param_force:
50 -force
51 #end if
52 #if $adv_opts.param_auto_rt_FHWM:
53 -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
54 #end if
55 #if $adv_opts.param_auto_rt_SNThreshold:
56 -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
57 #end if
26 #end if 58 #end if
27 </command> 59 </command>
28 <inputs> 60 <inputs>
29 <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input raw data file" help="(-in)"/> 61 <param format="mzml" help="(-in) " label="Input raw data file" multiple="true" name="param_in" optional="False" size="30" type="data">
30 <param name="param_in_header" type="data" format="txt" optional="True" size="20" label="[for Waters data only] Read additional information from _HEADER.TXT. Provide one for each raw input file." help="(-in_header)"/> 62 <sanitizer>
31 <param name="param_pos" type="data" format="" optional="False" label="Input config file stating where to find signal" help="(-pos)"/> 63 <valid initial="string.printable">
32 <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)"/> 64 <remove value="'"/>
33 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol)"/> 65 <remove value="&quot;"/>
34 <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)"/> 66 </valid>
35 <param name="param_enabled" type="boolean" truevalue="-auto_rt:enabled true" falsevalue="-auto_rt:enabled false" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations." help="(-enabled)"/> 67 </sanitizer>
36 <expand macro="advanced_options"> 68 </param>
37 <param name="param_out_separator" type="text" size="20" value="," label="Separator character for output CSV file." help="(-out_separator)"/> 69 <param format="txt" help="(-in_header) Provide one for each raw input file" label="[for Waters data only] Read additional information from _HEADER.TXT" multiple="true" name="param_in_header" optional="True" size="30" type="data">
38 <param name="param_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]. Gaussian smoothing filter with this width is applied to TIC." help="(-FHWM)"/> 70 <sanitizer>
39 <param name="param_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking. Higher thesholds will result in less peaks." help="(-SNThreshold)"/> 71 <valid initial="string.printable">
40 </expand> 72 <remove value="'"/>
41 </inputs> 73 <remove value="&quot;"/>
42 <outputs> 74 </valid>
43 <data name="param_out" label="Output quantitation file (multiple columns for each input compound)" format="tabular"/> 75 </sanitizer>
44 <data name="param_out_debug_TIC" label="Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions" format="mzML"/> 76 </param>
45 </outputs> 77 <param format="tabular" help="(-pos) " label="Input config file stating where to find signal" name="param_pos" optional="False" type="data"/>
46 <help>**What it does** 78 <param help="(-rt_tol) " label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" name="param_rt_tol" type="float" value="3.0"/>
47 79 <param help="(-mz_tol) " label="m/z tolerance in [ppm] for finding a peak" name="param_mz_tol" type="float" value="10.0"/>
48 Extracts intensities from dedicates positions in a LC/MS map 80 <param help="(-rt_collect) " label="# of scans up &amp; down in RT from highest point for ppm estimation in result" name="param_rt_collect" type="integer" value="1"/>
81 <param checked="false" falsevalue="" help="(-enabled) " label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" name="param_auto_rt_enabled" optional="True" truevalue="-auto_rt:enabled" type="boolean"/>
82 <expand macro="advanced_options">
83 <param help="(-out_separator) " label="Separator character for output CSV file" name="param_out_separator" size="30" type="text" value=",">
84 <sanitizer>
85 <valid initial="string.printable">
86 <remove value="'"/>
87 <remove value="&quot;"/>
88 </valid>
89 </sanitizer>
90 </param>
91 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
92 <param help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC" label="Expected full width at half-maximum of each raw RT peak in [s]" name="param_auto_rt_FHWM" type="float" value="5.0"/>
93 <param help="(-SNThreshold) Higher thesholds will result in less peaks" label="S/N threshold for a smoothed raw peak to pass peak picking" name="param_auto_rt_SNThreshold" type="float" value="5.0"/>
94 </expand>
95 </inputs>
96 <outputs>
97 <data format="tabular" name="param_out"/>
98 <data format="mzml" name="param_auto_rt_out_debug_TIC"/>
99 </outputs>
100 <help>Extracts intensities from dedicates positions in a LC/MS map
49 101
50 102
51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html 103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html</help>
52 104 </tool>
53 @REFERENCES@
54 </help>
55 </tool>