Mercurial > repos > galaxyp > openms_rtpredict

comparison RTPredict.xml @ 1:ad805b03ddf8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:55:48 -0400
parents 44f9dcfd2542
children 1eb2400e3f61
comparison
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0:44f9dcfd2542 1:ad805b03ddf8
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <tool id="RTPredict" name="RTPredict" version="2.1.0"> 4 <tool id="RTPredict" name="RTPredict" version="2.2.0">
5 <description>Predicts retention times for peptides using a model trained by RTModel.</description> 5 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RTPredict</token> 7 <token name="@EXECUTABLE@">RTPredict</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
15 #if $param_in_id: 15 #if $param_in_id:
16 -in_id $param_in_id 16 -in_id $param_in_id
17 #end if 17 #end if
18 #if $param_in_text: 18 #if $param_in_text:
19 -in_text $param_in_text 19 -in_text $param_in_text
20 #end if
21 #if $param_in_oligo_params:
22 -in_oligo_params $param_in_oligo_params
23 #end if
24 #if $param_in_oligo_trainset:
25 -in_oligo_trainset $param_in_oligo_trainset
20 #end if 26 #end if
21 #if $param_svm_model: 27 #if $param_svm_model:
22 -svm_model $param_svm_model 28 -svm_model $param_svm_model
23 #end if 29 #end if
24 #if $param_total_gradient_time: 30 #if $param_total_gradient_time:
49 #end if 55 #end if
50 </command> 56 </command>
51 <inputs> 57 <inputs>
52 <param name="param_in_id" type="data" format="idxml" optional="True" label="Peptides with precursor information" help="(-in_id) "/> 58 <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) "/> 59 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text) "/>
60 <param name="param_in_oligo_params" type="data" format="paramXML" optional="True" label="input file with additional model parameters when using the OLIGO kernel" help="(-in_oligo_params) "/>
61 <param name="param_in_oligo_trainset" type="data" format="txt" optional="True" label="input file with the used training dataset when using the OLIGO kernel" help="(-in_oligo_trainset) "/>
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) "/> 62 <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) "/> 63 <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"> 64 <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) "/> 65 <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) "/> 66 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>