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comparison AdditiveSeries.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="AdditiveSeries" name="AdditiveSeries" 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>Computes an additive series to quantify a peptide in a set of samples.</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="AdditiveSeries" name="AdditiveSeries" version="2.0.0">
5 <token name="@EXECUTABLE@">AdditiveSeries</token> 5 <description>Computes an additive series to quantify a peptide in a set of samples.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">AdditiveSeries</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>AdditiveSeries 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>AdditiveSeries
11 14
12 -in ${param_in} 15 -in
13 -out ${param_out} 16 #for token in $param_in:
14 -mz_tolerance ${param_mz_tolerance} 17 $token
15 -rt_tolerance ${param_rt_tolerance} 18 #end for
16 -concentrations ${param_concentrations} 19 #if $param_out:
17 -feature_rt ${param_feature_rt} 20 -out $param_out
18 -feature_mz ${param_feature_mz} 21 #end if
19 -standard_rt ${param_standard_rt} 22 #if $param_mz_tolerance:
20 -standard_mz ${param_standard_mz} 23 -mz_tolerance $param_mz_tolerance
21 -threads \${GALAXY_SLOTS:-24} 24 #end if
22 ${param_write_gnuplot_output} 25 #if $param_rt_tolerance:
23 -plot:out_gp ${param_out_gp} 26 -rt_tolerance $param_rt_tolerance
27 #end if
28
29 #if $rep_param_concentrations:
30 -concentrations
31 #for token in $rep_param_concentrations:
32 #if &quot; &quot; in str(token):
33 &quot;$token.param_concentrations&quot;
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 -threads \${GALAXY_SLOTS:-24}
52 #if $param_plot_write_gnuplot_output:
53 -plot:write_gnuplot_output
54 #end if
55 #if $param_plot_out_gp:
56 -plot:out_gp &quot;$param_plot_out_gp&quot;
57 #end if
58 #if $adv_opts.adv_opts_selector=='advanced':
59 #if $adv_opts.param_force:
60 -force
61 #end if
62 #end if
24 </command> 63 </command>
25 <inputs> 64 <inputs>
26 <param name="param_in" type="data" format="featureXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/> 65 <param format="xml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
27 <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance)"/> 66 <sanitizer>
28 <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance)"/> 67 <valid initial="string.printable">
29 <param name="param_concentrations" type="text" size="20" value="0" label="List of spiked concentrations" help="(-concentrations)"/> 68 <remove value="'"/>
30 <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt)"/> 69 <remove value="&quot;"/>
31 <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz)"/> 70 </valid>
32 <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt)"/> 71 </sanitizer>
33 <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz)"/> 72 </param>
34 <param name="param_write_gnuplot_output" type="boolean" truevalue="-plot:write_gnuplot_output true" falsevalue="-plot:write_gnuplot_output false" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output)"/> 73 <param help="(-mz_tolerance) " label="Tolerance in m/z dimension" name="param_mz_tolerance" type="float" value="1.0"/>
35 <param name="param_out_gp" type="text" size="20" label="base file name (3 files with different extensions are created)" help="(-out_gp)"/> 74 <param help="(-rt_tolerance) " label="Tolerance in RT dimension" name="param_rt_tolerance" type="float" value="1.0"/>
36 </inputs> 75 <repeat min="1" name="rep_param_concentrations" title="param_concentrations">
37 <outputs> 76 <param help="(-concentrations) " label="List of spiked concentrations" name="param_concentrations" size="30" type="text" value="0">
38 <data name="param_out" label="output XML file containg regression line and confidence interval" format="xml"/> 77 <sanitizer>
39 </outputs> 78 <valid initial="string.printable">
40 <help>**What it does** 79 <remove value="'"/>
41 80 <remove value="&quot;"/>
42 Computes an additive series to quantify a peptide in a set of samples. 81 </valid>
82 </sanitizer>
83 </param>
84 </repeat>
85 <param help="(-feature_rt) " label="RT position of the feature" name="param_feature_rt" type="float" value="-1.0"/>
86 <param help="(-feature_mz) " label="m/z position of the feature" name="param_feature_mz" type="float" value="-1.0"/>
87 <param help="(-standard_rt) " label="RT position of the standard" name="param_standard_rt" type="float" value="-1.0"/>
88 <param help="(-standard_mz) " label="m/z position of the standard" name="param_standard_mz" type="float" value="-1.0"/>
89 <param checked="false" falsevalue="" help="(-write_gnuplot_output) " label="Flag that activates the GNUplot output" name="param_plot_write_gnuplot_output" optional="True" truevalue="-plot:write_gnuplot_output" type="boolean"/>
90 <param help="(-out_gp) " label="base file name (3 files with different extensions are created)" name="param_plot_out_gp" size="30" type="text">
91 <sanitizer>
92 <valid initial="string.printable">
93 <remove value="'"/>
94 <remove value="&quot;"/>
95 </valid>
96 </sanitizer>
97 </param>
98 <expand macro="advanced_options">
99 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
100 </expand>
101 </inputs>
102 <outputs>
103 <data format="xml" name="param_out"/>
104 </outputs>
105 <help>Computes an additive series to quantify a peptide in a set of samples.
43 106
44 107
45 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html 108 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help>
46 109 </tool>
47 @REFERENCES@
48 </help>
49 </tool>