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comparison tandem.xml @ 15:0faaab4f192a draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:47:05 -0400
parents 9d6e0ad4d600
children 63b15b77e56c
comparison
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14:9d6e0ad4d600 15:0faaab4f192a
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0"> 1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1">
2 <description>Run an X!Tandem Search</description>
3 <requirements>
4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4.3">protk</requirement>
6 </requirements>
7 <command>
8 #if $database.source_select=="built_in":
9 tandem_search.rb -d $database.dbkey
10 #else
11 tandem_search.rb -d $database.fasta_file
12 #end if
2 13
3 <requirements> 14 #if $tandem_params.source_select=="built_in":
4 <container type="docker">iracooke/protk-1.4.1</container> 15 -T $tandem_params.paramskey
5 <requirement type="package" version="1.4">protk</requirement> 16 #else
6 </requirements> 17 -T $tandem_params.params_file
7 18 #end if
8 <description>Run an X!Tandem Search</description>
9
10 <command>
11 #if $database.source_select=="built_in":
12 tandem_search.rb -d $database.dbkey
13 #else
14 tandem_search.rb -d $database.fasta_file
15 #end if
16
17 #if $tandem_params.source_select=="built_in":
18 -T $tandem_params.paramskey
19 #else
20 -T $tandem_params.params_file
21 #end if
22 19
23 20
24 --var-mods=' 21 --var-mods='
25 $variable_mods 22 $variable_mods
26 #for $custom_variable_mod in $custom_variable_mods: 23 #for $custom_variable_mod in $custom_variable_mods:
27 ,${custom_variable_mod.custom_mod} 24 ,${custom_variable_mod.custom_mod}
28 #end for 25 #end for
29 ' 26 '
30 27
31 --fix-mods=' 28 --fix-mods='
32 $fixed_mods 29 $fixed_mods
33 #for $custom_fix_mod in $custom_fix_mods: 30 #for $custom_fix_mod in $custom_fix_mods:
34 ,${custom_fix_mod.custom_mod} 31 ,${custom_fix_mod.custom_mod}
35 #end for 32 #end for
36 ' 33 '
37 34
38 $input_file -o $output -r 35 $input_file -o $output -r
39 36
40 --enzyme=$enzyme 37 --enzyme=$enzyme
41 38
42 --precursor-ion-tol-units=$precursor_tolu 39 --precursor-ion-tol-units=$precursor_tolu
40 -v $missed_cleavages
41 -f $fragment_ion_tol
42 -p $precursor_ion_tol
43 $allow_multi_isotope_search
44 $acetyl_protein_nterm
45 $cleavage_semi
46 $keep_spectra
47 --threads "\${GALAXY_SLOTS:-12}"
43 48
44 -v $missed_cleavages 49 </command>
50 <inputs>
51 <conditional name="database">
52 <param name="source_select" type="select" label="Database source">
53 <option value="built_in">Built-In</option>
54 <option value="input_ref" selected="true">Your Upload File</option>
55 </param>
56 <when value="built_in">
57 <param name="dbkey" type="select" format="text" >
58 <label>Database</label>
59 <options from_file="pepxml_databases.loc">
60 <column name="name" index="0" />
61 <column name="value" index="2" />
62 </options>
63 </param>
64 </when>
65 <when value="input_ref">
66 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
67 </when>
68 </conditional>
69 <conditional name="tandem_params">
70 <param name="source_select" type="select" label="Baseline Parameters">
71 <option value="built_in" selected="true">Built-In</option>
72 <option value="input_ref">Custom parameter file</option>
73 </param>
74 <when value="built_in">
75 <param name="paramskey" type="select" format="text" >
76 <label>Paramset</label>
77 <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
78 <option value="isb_native">ISB Native</option>
79 <option value="gpm">GPM</option>
80 </param>
81 </when>
82 <when value="input_ref">
83 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
84 </when>
85 </conditional>
45 86
46 -f $fragment_ion_tol 87 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
47 88
48 -p $precursor_ion_tol 89 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
90 clicking to select multiple items">
91 <options from_file="tandem_mods.loc">
92 <column name="name" index="0" />
93 <column name="value" index="2" />
94 </options>
95 </param>
49 96
50 $allow_multi_isotope_search 97 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
98 <param name="custom_mod" type="text">
99 </param>
100 </repeat>
51 101
52 $acetyl_protein_nterm 102 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
103 clicking to select multiple items">
104 <options from_file="tandem_mods.loc">
105 <column name="name" index="0" />
106 <column name="value" index="2" />
107 </options>
108 </param>
53 109
54 $cleavage_semi 110 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
111 <param name="custom_mod" type="text">
112 </param>
113 </repeat>
55 114
56 $keep_spectra 115 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
116 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
117 <label>Missed Cleavages Allowed</label>
118 <option value="0">0</option>
119 <option value="1">1</option>
120 <option selected="true" value="2">2</option>
121 </param>
57 122
58 --threads $threads 123 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
59 124 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
60 </command>
61 125
62 <inputs> 126 <param name="enzyme" type="select" format="text">
63 <conditional name="database"> 127 <label>Enzyme</label>
64 <param name="source_select" type="select" label="Database source"> 128 <option value="[R]__pc__{P}">argc - [R]|{P}</option>
65 <option value="built_in">Built-In</option> 129 <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
66 <option value="input_ref" selected="true">Your Upload File</option> 130 <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option>
67 </param> 131 <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
68 <when value="built_in"> 132 <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
69 <param name="dbkey" type="select" format="text" > 133 <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
70 <label>Database</label> 134 <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
71 <options from_file="pepxml_databases.loc"> 135 <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
72 <column name="name" index="0" /> 136 <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
73 <column name="value" index="2" /> 137 <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
74 </options> 138 <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
75 </param> 139 <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
76 </when> 140 <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
77 <when value="input_ref"> 141 <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
78 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> 142 <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
79 </when> 143 <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
80 </conditional> 144 <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
81 145 <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
82 <conditional name="tandem_params"> 146 <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
83 <param name="source_select" type="select" label="Baseline Parameters"> 147 <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
84 <option value="built_in" selected="true">Built-In</option> 148 <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
85 <option value="input_ref">Custom parameter file</option> 149 <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
86 </param> 150 <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
87 <when value="built_in"> 151 </param>
88 <param name="paramskey" type="select" format="text" >
89 <label>Paramset</label>
90 <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
91 <option value="isb_native">ISB Native</option>
92 <option value="gpm">GPM</option>
93 </param>
94 </when>
95 <when value="input_ref">
96 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
97 </when>
98 </conditional>
99 152
100 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/> 153 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
101 154 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
102 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while 155 <param name="precursor_tolu" type="select" format="text">
103 clicking to select multiple items"> 156 <label>Precursor Ion Tolerance Units</label>
104 <options from_file="tandem_mods.loc"> 157 <option value="ppm">ppm</option>
105 <column name="name" index="0" /> 158 <option value="Da">Da</option>
106 <column name="value" index="2" /> 159 </param>
107 </options> 160 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
108 </param> 161 </inputs>
109 162 <outputs>
110 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> 163 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
111 <param name="custom_mod" type="text"> 164 </outputs>
112 </param> 165 <tests>
113 </repeat> 166 <!-- Just test that the tool runs and produces vaguely correct output -->
114 167 <test>
115 168 <param name="source_select" value="input_ref"/>
116 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while 169 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
117 clicking to select multiple items"> 170 <param name="input_file" value="tiny.mzML" format="mzml"/>
118 <options from_file="tandem_mods.loc"> 171 <output name="output" format="tandem">
119 <column name="name" index="0" /> 172 <assert_contents>
120 <column name="value" index="2" /> 173 <has_text text="tandem-style" />
121 </options> 174 </assert_contents>
122 </param> 175 </output>
123 176 </test>
124 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> 177 </tests>
125 <param name="custom_mod" type="text">
126 </param>
127 </repeat>
128
129 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
130
131
132 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
133 <label>Missed Cleavages Allowed</label>
134 <option value="0">0</option>
135 <option value="1">1</option>
136 <option selected="true" value="2">2</option>
137 </param>
138
139 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
140
141 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
142
143 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
144
145 <param name="enzyme" type="select" format="text">
146 <label>Enzyme</label>
147 <option value="[R]__pc__{P}">argc - [R]|{P}</option>
148 <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
149 <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option>
150 <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
151 <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
152 <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
153 <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
154 <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
155 <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
156 <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
157 <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
158 <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
159 <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
160 <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
161 <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
162 <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
163 <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
164 <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
165 <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
166 <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
167 <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
168 <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
169 <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
170 </param>
171
172
173 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
174
175 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
176 <param name="precursor_tolu" type="select" format="text">
177 <label>Precursor Ion Tolerance Units</label>
178 <option value="ppm">ppm</option>
179 <option value="Da">Da</option>
180 </param>
181
182 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
183
184 </inputs>
185
186
187 <outputs>
188 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
189 </outputs>
190
191 <tests>
192 <!-- Just test that the tool runs and produces vaguely correct output -->
193 <test>
194 <param name="source_select" value="input_ref"/>
195 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
196 <param name="input_file" value="tiny.mzML" format="mzml"/>
197 <output name="output" format="tandem">
198 <assert_contents>
199 <has_text text="tandem-style" />
200 </assert_contents>
201 </output>
202 </test>
203 </tests>
204 <help> 178 <help>
205 179
206 **What it does** 180 **What it does**
207 181
208 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. 182 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.