Mercurial > repos > galaxyp > openms_ticcalculator

comparison TICCalculator.xml @ 1:1373f6071423 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:48:23 -0400
parents cb4738f26b96
children 11fc1eb69276
comparison
equal deleted inserted replaced
0:cb4738f26b96 1:1373f6071423
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="TICCalculator" name="TICCalculator" version="2.1.0"> 4 <tool id="TICCalculator" name="TICCalculator" version="2.2.0.1">
5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description> 5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">TICCalculator</token> 7 <token name="@EXECUTABLE@">TICCalculator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_read_method: 18 #if $param_read_method:
19 -read_method $param_read_method 19 -read_method
20 #if " " in str($param_read_method):
21 "$param_read_method"
22 #else
23 $param_read_method
24 #end if
20 #end if 25 #end if
21 #if $param_loadData: 26 #if $param_loadData:
22 -loadData $param_loadData 27 -loadData
28 #if " " in str($param_loadData):
29 "$param_loadData"
30 #else
31 $param_loadData
32 #end if
23 #end if 33 #end if
24 #if $adv_opts.adv_opts_selector=='advanced': 34 #if $adv_opts.adv_opts_selector=='advanced':
25 #if $adv_opts.param_force: 35 #if $adv_opts.param_force:
26 -force 36 -force
27 #end if 37 #end if
28 #end if 38 #end if
29 &gt; $param_stdout 39 &gt; $param_stdout
30 </command> 40 </command>
31 <inputs> 41 <inputs>
32 <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/> 42 <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
33 <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) "> 43 <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) ">
34 <option value="regular" selected="true">regular</option> 44 <option value="regular" selected="true">regular</option>
35 <option value="indexed">indexed</option> 45 <option value="indexed">indexed</option>
36 <option value="indexed_parallel">indexed_parallel</option> 46 <option value="indexed_parallel">indexed_parallel</option>
37 <option value="streaming">streaming</option> 47 <option value="streaming">streaming</option>
45 <expand macro="advanced_options"> 55 <expand macro="advanced_options">
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 56 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
47 </expand> 57 </expand>
48 </inputs> 58 </inputs>
49 <outputs> 59 <outputs>
50 <data name="param_stdout" format="text" label="Output from stdout"/> 60 <data name="param_stdout" format="txt" label="Output from stdout"/>
51 </outputs> 61 </outputs>
52 <help>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). 62 <help>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
53 63
54 64
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_TICCalculator.html</help> 65 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_TICCalculator.html</help>
56 </tool> 66 </tool>