Mercurial > repos > galaxyp > openms_additiveseries

comparison AdditiveSeries.xml @ 0:24e8f13aef7e 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 12:49:49 -0500
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children d86b95a89b12
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-1:000000000000 0:24e8f13aef7e
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: [Quantitation]-->
4 <tool id="AdditiveSeries" name="AdditiveSeries" version="2.1.0">
5 <description>Computes an additive series to quantify a peptide in a set of samples.</description>
6 <macros>
7 <token name="@EXECUTABLE@">AdditiveSeries</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>AdditiveSeries
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_mz_tolerance:
23 -mz_tolerance $param_mz_tolerance
24 #end if
25 #if $param_rt_tolerance:
26 -rt_tolerance $param_rt_tolerance
27 #end if
28
29 #if $rep_param_concentrations:
30 -concentrations
31 #for token in $rep_param_concentrations:
32 #if " " in str(token):
33 "$token.param_concentrations"
34 #else
35 $token.param_concentrations
36 #end if
37 #end for
38 #end if
39 #if $param_feature_rt:
40 -feature_rt $param_feature_rt
41 #end if
42 #if $param_feature_mz:
43 -feature_mz $param_feature_mz
44 #end if
45 #if $param_standard_rt:
46 -standard_rt $param_standard_rt
47 #end if
48 #if $param_standard_mz:
49 -standard_mz $param_standard_mz
50 #end if
51 #if $param_plot_write_gnuplot_output:
52 -plot:write_gnuplot_output
53 #end if
54 #if $param_plot_out_gp:
55 -plot:out_gp "$param_plot_out_gp"
56 #end if
57 #if $adv_opts.adv_opts_selector=='advanced':
58 #if $adv_opts.param_force:
59 -force
60 #end if
61 #end if
62 </command>
63 <inputs>
64 <param name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
65 <sanitizer>
66 <valid initial="string.printable">
67 <remove value="'"/>
68 <remove value="&quot;"/>
69 </valid>
70 </sanitizer>
71 </param>
72 <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance) "/>
73 <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance) "/>
74 <repeat name="rep_param_concentrations" min="1" max="1" title="param_concentrations">
75 <param name="param_concentrations" type="text" size="30" value="0" label="List of spiked concentrations" help="(-concentrations) ">
76 <sanitizer>
77 <valid initial="string.printable">
78 <remove value="'"/>
79 <remove value="&quot;"/>
80 </valid>
81 </sanitizer>
82 </param>
83 </repeat>
84 <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt) "/>
85 <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz) "/>
86 <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt) "/>
87 <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz) "/>
88 <param name="param_plot_write_gnuplot_output" display="radio" type="boolean" truevalue="-plot:write_gnuplot_output" falsevalue="" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output) "/>
89 <param name="param_plot_out_gp" type="text" size="30" label="base file name (3 files with different extensions are created)" help="(-out_gp) ">
90 <sanitizer>
91 <valid initial="string.printable">
92 <remove value="'"/>
93 <remove value="&quot;"/>
94 </valid>
95 </sanitizer>
96 </param>
97 <expand macro="advanced_options">
98 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
99 </expand>
100 </inputs>
101 <outputs>
102 <data name="param_out" format="xml"/>
103 </outputs>
104 <help>Computes an additive series to quantify a peptide in a set of samples.
105
106
107 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help>
108 </tool>