comparison QCCalculator.xml @ 0:5759f19a8886 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:27:27 -0500
parents
children 9c2501dfde47
comparison
equal deleted inserted replaced
-1:000000000000 0:5759f19a8886
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="QCCalculator" name="QCCalculator" version="2.1.0">
5 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
6 <macros>
7 <token name="@EXECUTABLE@">QCCalculator</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>QCCalculator
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_id:
22 -id $param_id
23 #end if
24 #if $param_feature:
25 -feature $param_feature
26 #end if
27 #if $param_consensus:
28 -consensus $param_consensus
29 #end if
30 #if $param_remove_duplicate_features:
31 -remove_duplicate_features
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_in" type="data" format="mzml" optional="False" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help="(-in) "/>
41 <param name="param_id" type="data" format="idxml" optional="True" label="Input idXML file containing the identifications" help="(-id) Your identifications will be exported in an easy-to-read format"/>
42 <param name="param_feature" type="data" format="featurexml" optional="True" label="feature input file (this is relevant for most QC issues)" help="(-feature) "/>
43 <param name="param_consensus" type="data" format="consensusxml" optional="True" label="consensus input file (this is only used for charge state deconvoluted output" help="(-consensus) Use the consensusXML output form the DeCharger)"/>
44 <param name="param_remove_duplicate_features" display="radio" type="boolean" truevalue="-remove_duplicate_features" falsevalue="" checked="false" optional="True" label="This flag should be set, if you work with a set of merged features" help="(-remove_duplicate_features) "/>
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="qcml"/>
51 </outputs>
52 <help>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
53
54
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCCalculator.html</help>
56 </tool>