Mercurial > repos > galaxyp > openms_mascotadapter

comparison MascotAdapter.xml @ 7:fd960d61b64d 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 08:03:42 -0400
parents b0fcab295c60
children fb751f9c050b
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equal deleted inserted replaced
6:83b02507dcd2 7:fd960d61b64d
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>MascotAdapter 13 <command detect_errors="aggressive"><![CDATA[MascotAdapter
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_out: 18 #if $param_out:
138 #if $adv_opts.adv_opts_selector=='advanced': 138 #if $adv_opts.adv_opts_selector=='advanced':
139 #if $adv_opts.param_force: 139 #if $adv_opts.param_force:
140 -force 140 -force
141 #end if 141 #end if
142 #end if 142 #end if
143 </command> 143 ]]></command>
144 <inputs> 144 <inputs>
145 <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/> 145 <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
146 <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/> 146 <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
147 <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/> 147 <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
148 <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) "> 148 <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">
335 <data name="param_out" format="data"/> 335 <data name="param_out" format="data"/>
336 </outputs> 336 </outputs>
337 <help>Annotates MS/MS spectra using Mascot. 337 <help>Annotates MS/MS spectra using Mascot.
338 338
339 339
340 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MascotAdapter.html</help> 340 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MascotAdapter.html</help>
341 </tool> 341 </tool>