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comparison RTPredict.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
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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="RTPredict" name="RTPredict" 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>Predicts retention times for peptides using a model trained by RTModel.</description> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <macros> 4 <tool id="RTPredict" name="RTPredict" version="2.0.0">
5 <token name="@EXECUTABLE@">RTPredict</token> 5 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">RTPredict</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>RTPredict 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RTPredict
11 14
12 -in_id ${param_in_id} 15 #if $param_in_id:
13 -in_text ${param_in_text} 16 -in_id $param_in_id
14 -svm_model ${param_svm_model} 17 #end if
15 -total_gradient_time ${param_total_gradient_time} 18 #if $param_in_text:
16 -threads \${GALAXY_SLOTS:-24} 19 -in_text $param_in_text
17 -out_id:file ${param_file} 20 #end if
18 -out_id:positive ${param_positive} 21 #if $param_svm_model:
19 -out_id:negative ${param_negative} 22 -svm_model $param_svm_model
20 -out_text:file ${param_file} 23 #end if
24 #if $param_total_gradient_time:
25 -total_gradient_time $param_total_gradient_time
26 #end if
27 -threads \${GALAXY_SLOTS:-24}
28 #if $param_out_id_file:
29 -out_id:file $param_out_id_file
30 #end if
31 #if $param_out_id_positive:
32 -out_id:positive $param_out_id_positive
33 #end if
34 #if $param_out_id_negative:
35 -out_id:negative $param_out_id_negative
36 #end if
37 #if $param_out_text_file:
38 -out_text:file $param_out_text_file
39 #end if
21 #if $adv_opts.adv_opts_selector=='advanced': 40 #if $adv_opts.adv_opts_selector=='advanced':
22 -max_number_of_peptides ${adv_opts.param_max_number_of_peptides} 41 #if $adv_opts.param_max_number_of_peptides:
23 ${adv_opts.param_rewrite_peptideidentification_rtmz} 42 -max_number_of_peptides $adv_opts.param_max_number_of_peptides
43 #end if
44 #if $adv_opts.param_force:
45 -force
46 #end if
47 #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
48 -out_id:rewrite_peptideidentification_rtmz
49 #end if
24 #end if 50 #end if
25 </command> 51 </command>
26 <inputs> 52 <inputs>
27 <param name="param_in_id" type="data" format="idXML" optional="True" label="Peptides with precursor information" help="(-in_id)"/> 53 <param format="xml" help="(-in_id) " label="Peptides with precursor information" name="param_in_id" optional="True" type="data"/>
28 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text)"/> 54 <param format="txt" help="(-in_text) " label="Peptides as text-based file" name="param_in_text" optional="True" type="data"/>
29 <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 format="txt" help="(-svm_model) " label="svm model in libsvm format (can be produced by RTModel)" name="param_svm_model" optional="False" type="data"/>
30 <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 <param help="(-total_gradient_time) " label="The time (in seconds) of the gradient (peptide RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
31 <expand macro="advanced_options"> 57 <expand macro="advanced_options">
32 <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 help="(-max_number_of_peptides) " label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" name="param_max_number_of_peptides" type="integer" value="100000"/>
33 <param name="param_rewrite_peptideidentification_rtmz" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz true" falsevalue="-out_id:rewrite_peptideidentification_rtmz false" 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)"/> 59 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
34 </expand> 60 <param checked="false" falsevalue="" help="(-rewrite_peptideidentification_rtmz) " label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" name="param_out_id_rewrite_peptideidentification_rtmz" optional="True" truevalue="-out_id:rewrite_peptideidentification_rtmz" type="boolean"/>
35 </inputs> 61 </expand>
36 <outputs> 62 </inputs>
37 <data name="param_file" label="Output file with peptide RT prediction" format="idXML"/> 63 <outputs>
38 <data name="param_positive" label="Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well." format="idXML"/> 64 <data format="xml" name="param_out_id_file"/>
39 <data name="param_negative" label="Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well." format="idXML"/> 65 <data format="xml" name="param_out_id_positive"/>
40 <data name="param_file" label="Output file with predicted RT values" format="tabular"/> 66 <data format="xml" name="param_out_id_negative"/>
41 </outputs> 67 <data format="tabular" name="param_out_text_file"/>
42 <help>**What it does** 68 </outputs>
43 69 <help>Predicts retention times for peptides using a model trained by RTModel.
44 Predicts retention times for peptides using a model trained by RTModel.
45 70
46 71
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html 72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
48 73 </tool>
49 @REFERENCES@
50 </help>
51 </tool>