Mercurial > repos > galaxyp > openms_phosphoscoring

comparison PhosphoScoring.xml @ 7:3392cf4c19bb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 07:53:16 -0400
parents 98363174ac01
children 4c583fde2a28
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6:2d50765b7567 7:3392cf4c19bb
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>PhosphoScoring 13 <command detect_errors="aggressive"><![CDATA[PhosphoScoring
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_id: 18 #if $param_id:
41 #if $adv_opts.adv_opts_selector=='advanced': 41 #if $adv_opts.adv_opts_selector=='advanced':
42 #if $adv_opts.param_force: 42 #if $adv_opts.param_force:
43 -force 43 -force
44 #end if 44 #end if
45 #end if 45 #end if
46 </command> 46 ]]></command>
47 <inputs> 47 <inputs>
48 <param name="param_in" type="data" format="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/> 48 <param name="param_in" type="data" format="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/>
49 <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) "/> 49 <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) "/>
50 <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/> 50 <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/>
51 <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) "> 51 <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) ">
62 <data name="param_out" format="idxml"/> 62 <data name="param_out" format="idxml"/>
63 </outputs> 63 </outputs>
64 <help>Scores potential phosphorylation sites in order to localize the most probable sites. 64 <help>Scores potential phosphorylation sites in order to localize the most probable sites.
65 65
66 66
67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PhosphoScoring.html</help> 67 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PhosphoScoring.html</help>
68 </tool> 68 </tool>