Mercurial > repos > galaxyp > morpheus

comparison morpheus.xml @ 3:12c5c3a50d4b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author galaxyp
date Thu, 19 Nov 2015 16:02:50 -0500
parents 1c8071d2ae6f
children a7c58067f5ee
comparison
equal deleted inserted replaced
2:1c8071d2ae6f 3:12c5c3a50d4b
1 <tool id="morpheus" name="Morpheus" version="1.171.1"> 1 <tool id="morpheus" name="Morpheus" version="1.171.2">
2 <description>database search algorithm for high-resolution tandem mass spectra</description> 2 <description>database search algorithm for high-resolution tandem mass spectra</description>
3 <macros> 3 <macros>
4 <xml name="modification_options"> 4 <xml name="modification_options">
5 <option value="carbamidomethylation of C">carbamidomethylation of C</option>
6 <option value="oxidation of M">oxidation of M</option>
7 <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option> 5 <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option>
8 <option value="acetylation of lysine">acetylation of lysine</option> 6 <option value="acetylation of lysine">acetylation of lysine</option>
9 <option value="phosphorylation of S">phosphorylation of S</option> 7 <option value="phosphorylation of S">phosphorylation of S</option>
10 <option value="phosphorylation of T">phosphorylation of T</option> 8 <option value="phosphorylation of T">phosphorylation of T</option>
11 <option value="phosphorylation of Y">phosphorylation of Y</option> 9 <option value="phosphorylation of Y">phosphorylation of Y</option>
28 <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option> 26 <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option>
29 <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option> 27 <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option>
30 <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option> 28 <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option>
31 <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option> 29 <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option>
32 </xml> 30 </xml>
31 <xml name="variable_modification_options">
32 <option value="oxidation of M" selected="true">oxidation of M</option>
33 <option value="carbamidomethylation of C">carbamidomethylation of C</option>
34 <expand macro="modification_options"/>
35 </xml>
36 <xml name="fixed_modification_options">
37 <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option>
38 <option value="oxidation of M">oxidation of M</option>
39 <expand macro="modification_options"/>
40 </xml>
33 </macros> 41 </macros>
34 42
35 <requirements> 43 <requirements>
36 <requirement version="4.0">mono</requirement> 44 <requirement version="4.0">mono</requirement>
37 <requirement version="171">morpheus</requirement> 45 <requirement version="171">morpheus</requirement>
68 -fdr=$fdr 76 -fdr=$fdr
69 #end if 77 #end if
70 #if str($mvmi) != '': 78 #if str($mvmi) != '':
71 -mvmi=$mvmi 79 -mvmi=$mvmi
72 #end if 80 #end if
73 #if str($precmt) != 'None':
74 -precmt=$precmt
75 #end if
76 #if str($precmtv) != '': 81 #if str($precmtv) != '':
77 -precmtv=$precmtv 82 -precmtv=$precmtv
78 #end if 83 #end if
79 #if str($precmtu) != 'None': 84 #if str($precmtu) != 'None':
80 -precmtu=$precmtu 85 -precmtu=$precmtu
81 #end if 86 #end if
82 #if str( $advanced.adv_options_selector) == "set": 87 #if str( $advanced.adv_options_selector) == "set":
88 #if str($advanced.precmt) != 'None':
89 -precmt=$advanced.precmt
90 #end if
83 #if str($advanced.minprecz) != '': 91 #if str($advanced.minprecz) != '':
84 -minprecz=$advanced.minprecz 92 -minprecz=$advanced.minprecz
85 #end if 93 #end if
86 #if str($advanced.maxprecz) != '': 94 #if str($advanced.maxprecz) != '':
87 -maxprecz=$advanced.maxprecz 95 -maxprecz=$advanced.maxprecz
137 ]]></command> 145 ]]></command>
138 <inputs> 146 <inputs>
139 <param name="input" type="data" format="mzml" label='Indexed mzML' /> 147 <param name="input" type="data" format="mzml" label='Indexed mzML' />
140 <param name="searchdb" type="data" format="fasta,uniprotxml" label="MS Protein Search Database: UniProt Xml or Fasta"/> 148 <param name="searchdb" type="data" format="fasta,uniprotxml" label="MS Protein Search Database: UniProt Xml or Fasta"/>
141 <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications"> 149 <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications">
142 <expand macro="modification_options" /> 150 <expand macro="fixed_modification_options" />
143 </param> 151 </param>
144 <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications"> 152 <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications">
145 <expand macro="modification_options" /> 153 <expand macro="variable_modification_options" />
146 </param> 154 </param>
147 <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" /> 155 <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" />
148 <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" /> 156 <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" />
149 <param name="precmt" type="select" optional="true" label="Precursor Mass Type">
150 <option value="Monoisotopic">Monoisotopic</option>
151 <option value="Average">Average</option>
152 </param>
153 <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" /> 157 <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" />
154 <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units"> 158 <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units">
155 <option value="ppm" selected="true">ppm</option> 159 <option value="ppm" selected="true">ppm</option>
156 <option value="Da">Daltons</option> 160 <option value="Da">Daltons</option>
157 </param> 161 </param>
159 <param name="adv_options_selector" type="select" label="Set advanced options?" help="Provides additional controls"> 163 <param name="adv_options_selector" type="select" label="Set advanced options?" help="Provides additional controls">
160 <option value="set">Set</option> 164 <option value="set">Set</option>
161 <option value="do_not_set" selected="True">Do not set</option> 165 <option value="do_not_set" selected="True">Do not set</option>
162 </param> 166 </param>
163 <when value="set"> 167 <when value="set">
168 <param name="precmt" type="select" optional="true" label="Precursor Mass Type">
169 <option value="Monoisotopic">Monoisotopic</option>
170 <option value="Average">Average</option>
171 </param>
164 <param name="noup" type="boolean" truevalue="" falsevalue="-noup=True" checked="True" label="Use G-PTM with Uniprot Proteome Search Databases" /> 172 <param name="noup" type="boolean" truevalue="" falsevalue="-noup=True" checked="True" label="Use G-PTM with Uniprot Proteome Search Databases" />
165 <param name="minprecz" type="integer" value="2" optional="true" label="Minimum Unknown Precursor Charge State" /> 173 <param name="minprecz" type="integer" value="2" optional="true" label="Minimum Unknown Precursor Charge State" />
166 <param name="maxprecz" type="integer" value="4" optional="true" label="Maximum Unknown Precursor Charge State" /> 174 <param name="maxprecz" type="integer" value="4" optional="true" label="Maximum Unknown Precursor Charge State" />
167 <param name="at" type="float" value="" optional="true" min="0.0" label="Absolute MS/MS Intensity Threshold" /> 175 <param name="at" type="float" value="" optional="true" min="0.0" label="Absolute MS/MS Intensity Threshold" />
168 <param name="rt" type="float" value="" optional="true" min="0.0" label="Relative MS/MS Intensity Threshold" /> 176 <param name="rt" type="float" value="" optional="true" min="0.0" label="Relative MS/MS Intensity Threshold" />
169 <param name="mp" type="integer" value="" optional="true" min="-1" label="Maximum Number of MS/MS Peaks" help="to disable set to: -1"/> 177 <param name="mp" type="integer" value="400" optional="true" min="-1" label="Maximum Number of MS/MS Peaks" help="to disable set to: -1"/>
170 <param name="acs" type="boolean" truevalue="-acs=True" falsevalue="-acs=False" checked="true" optional="true" label="Assign Charge States" /> 178 <param name="acs" type="boolean" truevalue="-acs=True" falsevalue="-acs=False" checked="true" optional="true" label="Assign Charge States" />
171 <param name="di" type="boolean" truevalue="-di=True" falsevalue="-di=False" checked="true" optional="true" label="Deisotope" /> 179 <param name="di" type="boolean" truevalue="-di=True" falsevalue="-di=False" checked="false" optional="true" label="Deisotope" />
172 <param name="ad" type="select" optional="true" label="Append Decoys on the fly" 180 <param name="ad" type="select" optional="true" label="Create Target-Decoy Database On The Fly"
173 help="Set to No if Search Database ia a fasta that already includes decoys."> 181 help="Set to No if Search Database ia a fasta that already includes decoys.">
182 <option value="True" selected="true">Yes</option>
174 <option value="False">No</option> 183 <option value="False">No</option>
175 <option value="True">Yes</option>
176 </param> 184 </param>
177 <param name="mmc" type="integer" value="2" optional="true" min="0" max="20" label="Maximum Missed Cleavages" /> 185 <param name="mmc" type="integer" value="2" optional="true" min="0" max="20" label="Maximum Missed Cleavages" />
178 <param name="pmc" type="boolean" truevalue="-pmc=True" falsevalue="-pmc=False" checked="false" optional="true" label="Precursor Monoisotopic Peak Correction" /> 186 <param name="pmc" type="boolean" truevalue="-pmc=True" falsevalue="-pmc=False" checked="false" optional="true" label="Precursor Monoisotopic Peak Correction" />
179 <param name="minpmo" type="integer" value="" optional="true" label="Minimum Precursor Monoisotopic Peak Correction" /> 187 <param name="minpmo" type="integer" value="" optional="true" label="Minimum Precursor Monoisotopic Peak Correction" />
180 <param name="maxpmo" type="integer" value="" optional="true" label="Maximum Precursor Monoisotopic Peak Correction" /> 188 <param name="maxpmo" type="integer" value="" optional="true" label="Maximum Precursor Monoisotopic Peak Correction" />
190 <param name="imb" type="select" optional="true" label="Initiator Methionine Behavior"> 198 <param name="imb" type="select" optional="true" label="Initiator Methionine Behavior">
191 <option value="Variable">Variable</option> 199 <option value="Variable">Variable</option>
192 <option value="Retain">Retain</option> 200 <option value="Retain">Retain</option>
193 <option value="Cleave">Cleave</option> 201 <option value="Cleave">Cleave</option>
194 </param> 202 </param>
195 <param name="cmu" type="boolean" truevalue="-cmu=True" falsevalue="-cmu=False" checked="false" optional="true" label="Consider Modifications Unique" /> 203 <param name="cmu" type="boolean" truevalue="-cmu=True" falsevalue="-cmu=False" checked="false" optional="true" label="Consider Modified Forms as Unique Peptides" />
196 <param name="mmu" type="boolean" truevalue="-mmu=True" falsevalue="-mmu=False" checked="false" optional="true" label="Minimize Memory Usage" /> 204 <param name="mmu" type="boolean" truevalue="-mmu=True" falsevalue="-mmu=False" checked="false" optional="true" label="Minimize Memory Usage" />
197 </when> 205 </when>
198 <when value="do_not_set"/> 206 <when value="do_not_set"/>
199 </conditional> 207 </conditional>
200 </inputs> 208 </inputs>