Mercurial > repos > galaxyp > openms_rnpxlxicfilter

comparison RNPxlXICFilter.xml @ 0:4de461b0c05d 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 12:33:47 -0500
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children 8160f7ad51ed
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-1:000000000000 0:4de461b0c05d
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: [Utilities]-->
4 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="2.1.0">
5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
6 <macros>
7 <token name="@EXECUTABLE@">RNPxlXICFilter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RNPxlXICFilter
14
15 #if $param_control:
16 -control $param_control
17 #end if
18 #if $param_treatment:
19 -treatment $param_treatment
20 #end if
21 #if $param_fold_change:
22 -fold_change $param_fold_change
23 #end if
24 #if $param_rt_tol:
25 -rt_tol $param_rt_tol
26 #end if
27 #if $param_mz_tol:
28 -mz_tol $param_mz_tol
29 #end if
30 #if $param_out:
31 -out $param_out
32 #end if
33 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force:
35 -force
36 #end if
37 #end if
38 </command>
39 <inputs>
40 <param name="param_control" type="data" format="mzml" optional="False" label="input mzML file" help="(-control) "/>
41 <param name="param_treatment" type="data" format="mzml" optional="False" label="input mzML file" help="(-treatment) "/>
42 <param name="param_fold_change" type="float" value="2.0" label="fold change between XICs" help="(-fold_change) "/>
43 <param name="param_rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
44 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
45 <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) "/>
47 </expand>
48 </inputs>
49 <outputs>
50 <data name="param_out" format="mzml"/>
51 </outputs>
52 <help>Remove MS2 spectra from treatment based on the fold change between control and treatment.
53
54
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlXICFilter.html</help>
56 </tool>