Mercurial > repos > galaxyp > openms_ptpredict
comparison PTPredict.xml @ 0:56c8cc246637 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:19:47 -0500 |
| parents | |
| children | bd5ac30da605 |
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| -1:000000000000 | 0:56c8cc246637 |
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| 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="PTPredict" name="PTPredict" version="2.1.0"> | |
| 5 <description>predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">PTPredict</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>PTPredict | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 #if $param_out: | |
| 19 -out $param_out | |
| 20 #end if | |
| 21 #if $param_svm_model: | |
| 22 -svm_model $param_svm_model | |
| 23 #end if | |
| 24 #if $param_max_number_of_peptides: | |
| 25 -max_number_of_peptides $param_max_number_of_peptides | |
| 26 #end if | |
| 27 #if $adv_opts.adv_opts_selector=='advanced': | |
| 28 #if $adv_opts.param_force: | |
| 29 -force | |
| 30 #end if | |
| 31 #end if | |
| 32 </command> | |
| 33 <inputs> | |
| 34 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> | |
| 35 <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by PTModel)" help="(-svm_model) "/> | |
| 36 <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) <br>"/> | |
| 37 <expand macro="advanced_options"> | |
| 38 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 39 </expand> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data name="param_out" format="idxml"/> | |
| 43 </outputs> | |
| 44 <help>predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel | |
| 45 | |
| 46 | |
| 47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html</help> | |
| 48 </tool> |