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comparison RTPredict.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="RTPredict" name="RTPredict" version="2.0.0">
3 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
4 <macros>
5 <token name="@EXECUTABLE@">RTPredict</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>RTPredict
11
12 #if $param_in_id:
13 -in_id $param_in_id
14 #end if
15 #if $param_in_text:
16 -in_text $param_in_text
17 #end if
18 #if $param_svm_model:
19 -svm_model $param_svm_model
20 #end if
21 #if $param_total_gradient_time:
22 -total_gradient_time $param_total_gradient_time
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $param_out_id_file:
26 -out_id:file $param_out_id_file
27 #end if
28 #if $param_out_id_positive:
29 -out_id:positive $param_out_id_positive
30 #end if
31 #if $param_out_id_negative:
32 -out_id:negative $param_out_id_negative
33 #end if
34 #if $param_out_text_file:
35 -out_text:file $param_out_text_file
36 #end if
37 #if $adv_opts.adv_opts_selector=='advanced':
38 #if $adv_opts.param_max_number_of_peptides:
39 -max_number_of_peptides $adv_opts.param_max_number_of_peptides
40 #end if
41 #if $adv_opts.param_force:
42 -force
43 #end if
44 #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
45 -out_id:rewrite_peptideidentification_rtmz
46 #end if
47 #end if
48 </command>
49 <inputs>
50 <param name="param_in_id" type="data" format="idxml" optional="True" label="Peptides with precursor information" help="(-in_id) "/>
51 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text) "/>
52 <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) "/>
53 <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) "/>
54 <expand macro="advanced_options">
55 <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) "/>
56 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
57 <param name="param_out_id_rewrite_peptideidentification_rtmz" 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) "/>
58 </expand>
59 </inputs>
60 <outputs>
61 <data name="param_out_id_file" format="idxml"/>
62 <data name="param_out_id_positive" format="idxml"/>
63 <data name="param_out_id_negative" format="idxml"/>
64 <data name="param_out_text_file" format="tabular"/>
65 </outputs>
66 <help>**What it does**
67
68 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 <expand macro="references"/>
73 </tool>