Mercurial > repos > galaxyp > openms_cometadapter

comparison CometAdapter.xml @ 2:999615a63587 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:21:07 -0400
parents 921ff85ebfc6
children 2ffc94cb0766
comparison
equal deleted inserted replaced
1:475c4702fe58 2:999615a63587
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>CometAdapter 13 <command detect_errors="aggressive"><![CDATA[CometAdapter
14 14
15 -comet_executable comet
15 #if $param_in: 16 #if $param_in:
16 -in $param_in 17 -in $param_in
17 #end if 18 #end if
18 #if $param_out: 19 #if $param_out:
19 -out $param_out 20 -out $param_out
20 #end if 21 #end if
21 #if $param_database: 22 #if $param_database:
22 -database $param_database 23 -database $param_database
23 #end if
24 #if $param_comet_executable:
25 -comet_executable $param_comet_executable
26 #end if 24 #end if
27 #if $param_comet_version: 25 #if $param_comet_version:
28 -comet_version 26 -comet_version
29 #if " " in str($param_comet_version): 27 #if " " in str($param_comet_version):
30 "$param_comet_version" 28 "$param_comet_version"
212 #end if 210 #end if
213 #if $adv_opts.param_force: 211 #if $adv_opts.param_force:
214 -force 212 -force
215 #end if 213 #end if
216 #end if 214 #end if
217 </command> 215 -threads "\${GALAXY_SLOTS:-1}"
216 ]]></command>
218 <inputs> 217 <inputs>
219 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/> 218 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
220 <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file" help="(-database) "/> 219 <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file" help="(-database) "/>
221 <param name="param_comet_executable" type="data" format="txt" value="comet.exe" label="Comet executable of the installation" help="(-comet_executable) e.g. 'comet.exe'"/>
222 <param name="param_comet_version" display="radio" type="select" optional="False" value="2016.01 rev. 2" label="comet version: (year,version,revision)" help="(-comet_version) "> 220 <param name="param_comet_version" display="radio" type="select" optional="False" value="2016.01 rev. 2" label="comet version: (year,version,revision)" help="(-comet_version) ">
223 <option value="2016.01 rev. 2" selected="true">2016.01 rev. 2</option> 221 <option value="2016.01 rev. 2" selected="true">2016.01 rev. 2</option>
224 <option value="2016.01 rev. 3">2016.01 rev. 3</option> 222 <option value="2016.01 rev. 3">2016.01 rev. 3</option>
225 <option value="2017.01 rev. 0beta">2017.01 rev. 0beta</option> 223 <option value="2017.01 rev. 0beta">2017.01 rev. 0beta</option>
226 </param> 224 </param>
5412 <data name="param_pin_out" format="tabular"/> 5410 <data name="param_pin_out" format="tabular"/>
5413 </outputs> 5411 </outputs>
5414 <help>Annotates MS/MS spectra using Comet. 5412 <help>Annotates MS/MS spectra using Comet.
5415 5413
5416 5414
5417 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CometAdapter.html</help> 5415 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_CometAdapter.html</help>
5418 </tool> 5416 </tool>