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comparison macros.xml @ 41:3634c90301af draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit dea56622eb32b82c87dc87567dc89db3a787033d
author galaxyp
date Sat, 28 Oct 2017 04:16:50 -0400
parents 79e37eff006d
children 9e20c34298e3
comparison
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40:a72c48001f7c 41:3634c90301af
6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/> 7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
8 </stdio> 8 </stdio>
9 </xml> 9 </xml>
10 <token name="@GENERAL_PARAMETERS@"> 10 <token name="@GENERAL_PARAMETERS@">
11 -frag_tol "${precursor_options.fragment_tol}" 11 -frag_tol '${precursor_options.fragment_tol}'
12 ### -frag_ppm 12 -frag_ppm '${precursor_options.fragment_tol_units}'
13 -prec_tol "${precursor_options.precursor_ion_tol}" 13 -prec_tol '${precursor_options.precursor_ion_tol}'
14 -prec_ppm "${precursor_options.precursor_ion_tol_units}" 14 -prec_ppm '${precursor_options.precursor_ion_tol_units}'
15 15
16 -min_charge $precursor_options.min_charge 16 -min_charge $precursor_options.min_charge
17 -max_charge $precursor_options.max_charge 17 -max_charge $precursor_options.max_charge
18 -fi $precursor_options.forward_ion 18 -fi $precursor_options.forward_ion
19 -ri $precursor_options.reverse_ion 19 -ri $precursor_options.reverse_ion
124 <option value="1">Parts per million (ppm)</option> 124 <option value="1">Parts per million (ppm)</option>
125 <option value="2">Daltons</option> 125 <option value="2">Daltons</option>
126 </param> 126 </param>
127 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance" 127 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
128 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> 128 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
129 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" 129 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
130 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
131 <option value="1">Parts per million (ppm)</option>
132 <option value="2">Daltons</option>
133 </param>
134 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
130 help="Provide error value for fragment ions, based on instrument used"/> 135 help="Provide error value for fragment ions, based on instrument used"/>
131 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> 136 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
132 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> 137 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
133 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> 138 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
134 <option value="a">a</option> 139 <option value="a">a</option>