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comparison RTPredict.xml @ 0:44f9dcfd2542 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 12:56:29 -0500
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-1:000000000000 0:44f9dcfd2542
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: [Peptide property prediction]-->
4 <tool id="RTPredict" name="RTPredict" version="2.1.0">
5 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
6 <macros>
7 <token name="@EXECUTABLE@">RTPredict</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RTPredict
14
15 #if $param_in_id:
16 -in_id $param_in_id
17 #end if
18 #if $param_in_text:
19 -in_text $param_in_text
20 #end if
21 #if $param_svm_model:
22 -svm_model $param_svm_model
23 #end if
24 #if $param_total_gradient_time:
25 -total_gradient_time $param_total_gradient_time
26 #end if
27 #if $param_out_id_file:
28 -out_id:file $param_out_id_file
29 #end if
30 #if $param_out_id_positive:
31 -out_id:positive $param_out_id_positive
32 #end if
33 #if $param_out_id_negative:
34 -out_id:negative $param_out_id_negative
35 #end if
36 #if $param_out_text_file:
37 -out_text:file $param_out_text_file
38 #end if
39 #if $adv_opts.adv_opts_selector=='advanced':
40 #if $adv_opts.param_max_number_of_peptides:
41 -max_number_of_peptides $adv_opts.param_max_number_of_peptides
42 #end if
43 #if $adv_opts.param_force:
44 -force
45 #end if
46 #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
47 -out_id:rewrite_peptideidentification_rtmz
48 #end if
49 #end if
50 </command>
51 <inputs>
52 <param name="param_in_id" type="data" format="idxml" optional="True" label="Peptides with precursor information" help="(-in_id) "/>
53 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text) "/>
54 <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by RTModel)" help="(-svm_model) "/>
55 <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="The time (in seconds) of the gradient (peptide RT prediction)" help="(-total_gradient_time) "/>
56 <expand macro="advanced_options">
57 <param name="param_max_number_of_peptides" type="integer" value="100000" label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" help="(-max_number_of_peptides) "/>
58 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
59 <param name="param_out_id_rewrite_peptideidentification_rtmz" display="radio" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz" falsevalue="" checked="false" optional="True" label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" help="(-rewrite_peptideidentification_rtmz) "/>
60 </expand>
61 </inputs>
62 <outputs>
63 <data name="param_out_id_file" format="idxml"/>
64 <data name="param_out_id_positive" format="idxml"/>
65 <data name="param_out_id_negative" format="idxml"/>
66 <data name="param_out_text_file" format="tabular"/>
67 </outputs>
68 <help>Predicts retention times for peptides using a model trained by RTModel.
69
70
71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
72 </tool>