Mercurial > repos > galaxyp > openms_phosphoscoring
comparison PhosphoScoring.xml @ 0:0a1e6a367122 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:33:19 -0500 |
| parents | |
| children | e52a682b5b70 |
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| -1:000000000000 | 0:0a1e6a367122 |
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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: [ID Processing]--> | |
| 4 <tool id="PhosphoScoring" name="PhosphoScoring" version="2.1.0"> | |
| 5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">PhosphoScoring</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>PhosphoScoring | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 #if $param_id: | |
| 19 -id $param_id | |
| 20 #end if | |
| 21 #if $param_out: | |
| 22 -out $param_out | |
| 23 #end if | |
| 24 #if $param_fragment_mass_tolerance: | |
| 25 -fragment_mass_tolerance $param_fragment_mass_tolerance | |
| 26 #end if | |
| 27 #if $param_fragment_mass_unit: | |
| 28 -fragment_mass_unit $param_fragment_mass_unit | |
| 29 #end if | |
| 30 #if $param_max_peptide_length: | |
| 31 -max_peptide_length $param_max_peptide_length | |
| 32 #end if | |
| 33 #if $param_max_num_perm: | |
| 34 -max_num_perm $param_max_num_perm | |
| 35 #end if | |
| 36 #if $adv_opts.adv_opts_selector=='advanced': | |
| 37 #if $adv_opts.param_force: | |
| 38 -force | |
| 39 #end if | |
| 40 #end if | |
| 41 </command> | |
| 42 <inputs> | |
| 43 <param name="param_in" type="data" format="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/> | |
| 44 <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/> | |
| 45 <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/> | |
| 46 <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) "> | |
| 47 <option value="Da" selected="true">Da</option> | |
| 48 <option value="ppm">ppm</option> | |
| 49 </param> | |
| 50 <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/> | |
| 51 <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/> | |
| 52 <expand macro="advanced_options"> | |
| 53 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 54 </expand> | |
| 55 </inputs> | |
| 56 <outputs> | |
| 57 <data name="param_out" format="idxml"/> | |
| 58 </outputs> | |
| 59 <help>Scores potential phosphorylation sites in order to localize the most probable sites. | |
| 60 | |
| 61 | |
| 62 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PhosphoScoring.html</help> | |
| 63 </tool> |