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comparison msgfplus.xml @ 1:08b316ae9ec4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
author galaxyp
date Wed, 11 Nov 2015 16:13:39 -0500
parents dbc77b37e20f
children 159aa8cd779d
comparison
equal deleted inserted replaced
0:dbc77b37e20f 1:08b316ae9ec4
17 #set $input_name = $s.display_name 17 #set $input_name = $s.display_name
18 #set $output_name = $input_name.replace(".mzML", "") + ".mzid" 18 #set $output_name = $input_name.replace(".mzML", "") + ".mzid"
19 ln -s '$s' '${input_name}' && 19 ln -s '$s' '${input_name}' &&
20 ln -s '$d' '${db_name}' && 20 ln -s '$d' '${db_name}' &&
21 21
22 java -jar \$(which MSGFPlus.jar) 22 echo \\#Mods > Mods.txt &&
23 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
24 #for $mod in $common_mods.split(",")
25 echo '$mod.replace("_", ",")' >> Mods.txt &&
26 #end for
27
28 #for $mod in $custom_mods
29 echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
30 #end for
31
32 msgfjar=\$(which MSGFPlus.jar) &&
33 ( [ -f "\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) &&
34
35 java -jar \$msgfjar
23 -s '$input_name' 36 -s '$input_name'
24 -d '$db_name' 37 -d '$db_name'
25 -thread \${GALAXY_SLOTS:-1} 38 -thread \${GALAXY_SLOTS:-1}
26 39 -mod Mods.txt
27 -tda $tda 40 -tda $tda
28 -t $t$precursor_ion_tol_units 41 -t $t$precursor_ion_tol_units
29 -ti $advanced.isotope_low,$advanced.isotope_high 42 -ti $advanced.isotope_low,$advanced.isotope_high
30 -m $advanced.m 43 -m $advanced.m
31 -inst $inst 44 -inst $inst
72 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more."> 85 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more.">
73 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option> 86 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option>
74 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option> 87 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option>
75 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option> 88 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
76 </param> 89 </param>
77 <!-- 90
78 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> 91 <param name="common_fixed_modifications" type="select" label="Common Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
79 <options from_file="searchgui_mods.loc"> 92 <option value="C2H3N1O1_C_fix_any_Carbamidomethyl" selected="true">Carbamidomethyl C</option>
80 <column name="name" index="0" /> 93 <option value="144.102063_*_fix_N-term_iTRAQ4plex">iTRAQ 4-plex N-term</option>
81 <column name="value" index="0" /> 94 <option value="144.102063_K_fix_any_iTRAQ4plex">iTRAQ 4-plex K</option>
82 </options> 95 <option value="225.155833_*_fix_N-term_TMT6plex">TMT 2-plex N-term</option>
83 </param> 96 <option value="225.155833_K_fix_any_TMT6plex">TMT 2-plex K</option>
84 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> 97 <option value="229.162932_*_fix_N-term_TMT6plex">TMT 6-or-10-plex N-term</option>
85 <options from_file="searchgui_mods.loc"> 98 <option value="229.162932_K_fix_any_TMT6plex">TMT 6-or-10-plex K</option>
86 <column name="name" index="0" /> 99 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
87 <column name="value" index="0" /> 100 </param>
88 </options> 101 <param name="common_variable_modifications" type="select" label="Common Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
89 </param>--> 102 <option value="C2H2O1_K_opt_any_Acetyl">Acetylation K</option>
103 <option value="C2H2O_*_opt_Prot-N-term_Acetyl">Acetylation Protein N-term</option>
104 <option value="C2H3NO_C_opt_any_Carbamidomethyl">Carbamidomethyl C</option>
105 <option value="C2H3NO_*_opt_N-term_Carbamidomethyl">Carbamidomethyl N-term</option>
106 <option value="H-1N-1O1_N_opt_any_Deamidated">Deamidation N</option>
107 <option value="H-1N-1O1_Q_opt_any_Deamidated">Deamidation Q</option>
108 <option value="CH2_K_opt_any_Methyl">Methylation K</option>
109 <option value="O1_M_opt_any_Oxidation" selected="true">Oxidation M</option>
110 <option value="HO3P_S_opt_any_Phospho">Phosphorylation S</option>
111 <option value="HO3P_T_opt_any_Phospho">Phosphorylation T</option>
112 <option value="HO3P_Y_opt_any_Phospho">Phosphorylation Y</option>
113 <option value="H-2O-1_E_opt_N-term_Glu-&gt;pyro-Glu">Pyro-glu from E</option>
114 <option value="H-3N-1_Q_opt_N-term_Gln-&gt;pyro-Glu">Pyro-glu from Q</option>
115 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
116 </param>
117
118 <repeat name="custom_mods" title="Custom Modifications" help="Specify modifications with custom parameters">
119 <param name="formula_or_mass" type="text" label="Formula or Mass">
120 <sanitizer>
121 <valid initial="string.digits">
122 <add value="C"/>
123 <add value="H"/>
124 <add value="O"/>
125 <add value="N"/>
126 <add value="S"/>
127 <add value="P"/>
128 <add value="B"/><add value="r"/>
129 <add value="C"/><add value="l"/>
130 <add value="F"/><add value="e"/>
131 <add value="S"/>
132 <add value="."/>
133 <add value="-"/>
134 </valid>
135 </sanitizer>
136 </param>
137 <param name="aa_specificity" type="select" multiple="true" label="Amino Acid Specificity">
138 <option value="*" selected="true">Any</option>
139 <option value="A">A</option>
140 <option value="C">C</option>
141 <option value="D">D</option>
142 <option value="E">E</option>
143 <option value="F">F</option>
144 <option value="G">G</option>
145 <option value="H">H</option>
146 <option value="I">I</option>
147 <option value="K">K</option>
148 <option value="L">L</option>
149 <option value="M">M</option>
150 <option value="N">N</option>
151 <option value="P">P</option>
152 <option value="Q">Q</option>
153 <option value="R">R</option>
154 <option value="S">S</option>
155 <option value="T">T</option>
156 <option value="V">V</option>
157 <option value="W">W</option>
158 <option value="Y">Y</option>
159 </param>
160 <param name="fix_or_opt" type="select" label="Variable or Fixed?">
161 <option value="opt" selected="true">Variable</option>
162 <option value="fix">Fixed</option>
163 </param>
164 <param name="position_specificity" type="select" label="Positional Specificity">
165 <option value="any" selected="true">Any</option>
166 <option value="n-term">Peptide N-terminal</option>
167 <option value="c-term">Peptide C-terminal</option>
168 <option value="prot-n-term">Protein N-terminal</option>
169 <option value="prot-c-term">Protein C-terminal</option>
170 </param>
171 <param name="mod_name" type="text" label="Name" help="If this mod has an entry there in Unimod, this name should match its name there" />
172 </repeat>
90 173
91 <!-- MS-GF+ ADVANCED PARAMETERS --> 174 <!-- MS-GF+ ADVANCED PARAMETERS -->
92 <section name="advanced" title="Advanced Options"> 175 <section name="advanced" title="Advanced Options">
93 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/> 176 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/>
94 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/> 177 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/>
120 </outputs> 203 </outputs>
121 <tests> 204 <tests>
122 <test> 205 <test>
123 <param name="s" value="input/201208-378803.mzML" /> 206 <param name="s" value="input/201208-378803.mzML" />
124 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" /> 207 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
125 <output name="output" file="201208-378803-msgf.mzid" lines_diff="12" /> 208 <param name="tda" value="1" />
209 <param name="ntt" value="1" />
210 <param name="t" value="50" />
211 <param name="precursor_ion_tol_units" value="ppm" />
212 <param name="common_fixed_modifications" value="" />
213 <param name="common_variable_modifications" value="" />
214 <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />
126 </test> 215 </test>
127 <test> 216 <test>
128 <param name="s" value="input/201208-378803.mzML" /> 217 <param name="s" value="input/201208-378803.mzML" />
129 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" /> 218 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
130 <param name="tda" value="1" /> 219 <param name="tda" value="1" />
131 <param name="t" value="0.02" /> 220 <param name="t" value="0.02" />
132 <param name="precursor_ion_tol_units" value="Da" /> 221 <param name="precursor_ion_tol_units" value="Da" />
133 <param name="isotope_low" value="-1" /> 222 <param name="isotope_low" value="-1" />
134 <param name="isotope_high" value="0" /> 223 <param name="isotope_high" value="0" />
135 <param name="m" value="1" /> 224 <param name="m" value="3" />
136 <param name="inst" value="1" /> 225 <param name="inst" value="2" />
137 <param name="e" value="3" /> 226 <param name="e" value="3" />
138 <param name="ntt" value="1" />
139 <param name="protocol" value="2" /> 227 <param name="protocol" value="2" />
140 <param name="minLength" value="10" /> 228 <param name="minLength" value="10" />
141 <param name="maxLength" value="20" /> 229 <param name="maxLength" value="20" />
142 <param name="minCharge" value="2" /> 230 <param name="minCharge" value="2" />
143 <param name="maxCharge" value="6" /> 231 <param name="maxCharge" value="6" />
144 <param name="n" value="2" /> 232 <param name="n" value="2" />
145 <param name="addFeatures" value="1" /> 233 <param name="addFeatures" value="1" />
146 <output name="output" file="201208-378803-msgf-2mmu-semi-tryptic.mzid" lines_diff="12" /> 234
235 <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" />
236 <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" />
237
238 <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" />
239 <param name="custom_mods_0|aa_specificity" value="G" />
240 <param name="custom_mods_0|fix_or_opt" value="opt" />
241 <param name="custom_mods_0|position_specificity" value="c-term" />
242 <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" />
243
244 <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />
245 <param name="custom_mods_1|aa_specificity" value="CS" />
246 <param name="custom_mods_1|fix_or_opt" value="opt" />
247 <param name="custom_mods_1|position_specificity" value="any" />
248 <param name="custom_mods_1|mod_name" value="cGMP" />
249
250 <output name="output" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" />
147 </test> 251 </test>
148 </tests> 252 </tests>
149 <help> 253 <help>
150 **What it does** 254 **What it does**
151 255