Mercurial > repos > galaxyp > directag_and_tagrecon
comparison tools/directag_and_tagrecon.xml @ 0:45b68db74563 draft default tip
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author | galaxyp |
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date | Fri, 26 Sep 2014 18:49:37 -0400 |
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-1:000000000000 | 0:45b68db74563 |
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1 <tool id="directag_and_tagrecon" version="0.1.0" name="DirecTag and TagRecon"> | |
2 <requirements> | |
3 <requirement type="package" version="333">binaries_for_package_directag</requirement> | |
4 <requirement type="package" version="444">binaries_for_package_tagrecon</requirement> | |
5 </requirements> | |
6 | |
7 <description></description> | |
8 <command> | |
9 #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta" | |
10 #if $output_type.value == "mzid" | |
11 #set $output_ext="mzid" | |
12 #set $output_format="mzIdentML" | |
13 #else | |
14 #set $output_ext="pepXML" | |
15 #set $output_format="pepXML" | |
16 #end if | |
17 #set $input_name = $input.display_name | |
18 #set $tags_name = $input_name.split(".")[0] + ".tags" | |
19 #set $output_name = $input_name.split(".")[0] + "." + $output_ext | |
20 #set $static_mods_str = "" | |
21 #for $static_mod in $static_mods | |
22 #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass) | |
23 #end for | |
24 #set $dynamic_mods_str = "" | |
25 #set $dynamic_mod_index = 0 | |
26 #for $dynamic_mod in $dynamic_mods | |
27 #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass) | |
28 #set $dynamic_mod_index = $dynamic_mod_index + 1 | |
29 #end for | |
30 ln -s '$input' '${input_name}'; | |
31 ln -s '$input_database' '${db_name}'; | |
32 cp \${TAGRECON_UNIMOD_PATH:-${GALAXY_DATA_INDEX_DIR}/unimod.xml} .; | |
33 cp \${TAGRECON_BLOSUM_PATH:-${GALAXY_DATA_INDEX_DIR}/blosum62.fas} .; | |
34 directag '${input_name}' \ | |
35 -StaticMods '${static_mods_str}' \ | |
36 -DynamicMods '${dynamic_mods_str}' \ | |
37 -MaxDynamicMods '$max_dynamic_mods' \ | |
38 -MaxResults ${max_tags} \ | |
39 -FragmentMzTolerance ${tag_mz_tolerance} \ | |
40 #if $advanced_charge_options.specify | |
41 -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \ | |
42 #end if | |
43 #if $tag_weights.specify | |
44 -IntensityScoreWeight $tag_weights.intensity \ | |
45 -MzFidelityScoreWeight $tag_weights.mz \ | |
46 -ComplementScoreWeight $tag_weights.complement \ | |
47 #end if | |
48 ; | |
49 tagrecon -DecoyPrefix '${decoy_prefix}' \ | |
50 -ProteinDatabase '${db_name}' \ | |
51 -OutputFormat '${$output_format}' \ | |
52 -StaticMods '${static_mods_str}' \ | |
53 -DynamicMods '${dynamic_mods_str}' \ | |
54 -MaxDynamicMods '$max_dynamic_mods' \ | |
55 -CleavageRules '${protease}' \ | |
56 -MaxMissedCleavages ${max_missed_cleavages} \ | |
57 #if $advanced_cleavage_options.specify | |
58 -MinTerminiCleavages $advanced_cleavage_options.min_termini_cleavages \ | |
59 -UseNETAdjustment $advanced_cleavage_options.use_net_adjustment \ | |
60 #end if | |
61 #if $advanced_charge_options.specify | |
62 -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \ | |
63 #end if | |
64 #if $search_untagged.search | |
65 -SearchUntaggedSpectra true \ | |
66 -UntaggedSpectraPrecMZTol $search_untagged.precursor_mz_tolerance | |
67 #end if | |
68 '${tags_name}'; | |
69 mv '$output_name' output | |
70 </command> | |
71 <stdio> | |
72 <exit_code range="1:" level="fatal" description="Job Failed" /> | |
73 <regex match="^Could not find the default configuration file.*$" | |
74 source="both" | |
75 level="warning" /> | |
76 </stdio> | |
77 <inputs> | |
78 <conditional name="type"> | |
79 <param name="input_type" type="select" label="Input Type"> | |
80 <option value="mzml">mzML</option> | |
81 <option value="mzxml">mzXML</option> | |
82 <option value="mgf">mgf</option> | |
83 <option value="ms2">ms2</option> | |
84 </param> | |
85 <when value="mzml"> | |
86 <param format="mzml" name="input" type="data" label="Input mzML"/> | |
87 </when> | |
88 <when value="mzxml"> | |
89 <param format="mzxml" name="input" type="data" label="Input mzXML"/> | |
90 </when> | |
91 <when value="mgf"> | |
92 <param format="mgf" name="input" type="data" label="Input mgf"/> | |
93 </when> | |
94 <when value="ms2"> | |
95 <param format="ms2" name="input" type="data" label="Input ms2"/> | |
96 </when> | |
97 </conditional> | |
98 <param name="output_type" type="select" label="Output Type"> | |
99 <option value="raw_pepxml">pepXML</option> | |
100 <option value="mzid">mzIdentML</option> | |
101 </param> | |
102 <param format="fasta" name="input_database" type="data" label="Protein Database"/> | |
103 <param name="decoy_prefix" type="text" label="Decoy Prefix"/> | |
104 <repeat name="static_mods" title="Static Modifications (used by both directag and tagrecon) "> | |
105 <param name="aa" type="text" label="Amino Acid" /> | |
106 <param name="mass" type="float" label="Mass" value="0" /> | |
107 </repeat> | |
108 <repeat name="dynamic_mods" title="Dynamic Modifications (used by both directag and tagrecon)" max="7"> | |
109 <param name="motif" type="text" label="Amino Acid Motif" /> | |
110 <param name="mass" type="float" label="Mass" value="0" /> | |
111 </repeat> | |
112 <param name="max_dynamic_mods" type="integer" label="Maximum Dynamic Mods per Sequence" value="2" /> | |
113 <param name="tag_length" type="integer" label="Tag Length" value="3" help="A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare." /> | |
114 <param name="max_tags" type="integer" label="Maximum Number of Tags per Spectrum" value="20" /> | |
115 <param name="tag_mz_tolerance" type="float" label="Fragment m/z Tolerance during Tag Generation (Da/z)" value=".5" /> | |
116 <param name="protease" type="select" label="Protease"> | |
117 <options from_file="proteases.loc"> | |
118 <column name="name" index="0" /> | |
119 <column name="value" index="1" /> | |
120 </options> | |
121 </param> | |
122 <param name="max_missed_cleavages" label="Maximum Number of Missed Cleavages" type="integer" value="-1" /> | |
123 <conditional name="advanced_cleavage_options"> | |
124 <param name="specify" type="boolean" label="Specify advanced cleavage options" help="" truevalue="true" falsevalue="false" /> | |
125 <when value="false" /> | |
126 <when value="true"> | |
127 <param name="min_termini_cleavages" type="select" label="Minimum Termini Cleavages" value="2" help="A peptide must start after a cleavage and end before a cleavage. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified above."> | |
128 <option value="2">2</option> | |
129 <option value="1">1</option> | |
130 <option value="0">0</option> | |
131 </param> | |
132 <param name="use_net_adjustment" type="boolean" label="Use NET Adjustment" help="When enabled, TagRecon adds a probabilistic bonus to peptide scores depending on whether the peptides are fully-enzymatic, semi-enzymatic, or non-enzymatic." truevalue="true" falsevalue="false" /> | |
133 </when> | |
134 </conditional> | |
135 <conditional name="advanced_charge_options"> | |
136 <param name="specify" type="boolean" label="Specify Advanced Charge State Handling Options" help="" truevalue="true" falsevalue="false" /> | |
137 <when value="false" /> | |
138 <when value="true"> | |
139 <param name="use_ms_charge_state" type="boolean" label="Use Charge State from MS" truevalue="true" falsevalue="false" help="When enabled, DirecTag and TagRecon will not use their internal algorithm to determine charge state of a spectrum when it is available in the input file." /> | |
140 <!-- TODO: Add DuplicateSpectra, NumChargeStates --> | |
141 </when> | |
142 </conditional> | |
143 <!-- TODO: Advanced Peptide Filtering: Min/Max Peptide Mass/Length --> | |
144 <conditional name="tag_weights"> | |
145 <param name="specify" type="boolean" label="Override Default Tag Weighting" help="By default equal weights are assigned to intensity, m/z fidelity, and complement scores." truevalue="true" falsevalue="false" /> | |
146 <when value="false" /> | |
147 <when value="true"> | |
148 <param name="intensity" type="float" label="Intensity Score Weight" help="" value="1.0" /> | |
149 <param name="mz" type="float" label="m/z Fidelity Score Weight" help="" value="1.0" /> | |
150 <param name="complement" type="float" label="Complement Score Weight" help="" value="1.0" /> | |
151 </when> | |
152 </conditional> | |
153 <conditional name="search_untagged"> | |
154 <param name="search" type="boolean" label="Search Untagged Spectra" help="Search untagged spectra like a database search." truevalue="true" falsevalue="false" /> | |
155 <when value="false" /> | |
156 <when value="true"> | |
157 <param name="precursor_mz_tolerance" type="float" label="Untagged Spectra Precursor m/z Tolerance" value="1.25" /> | |
158 </when> | |
159 </conditional> | |
160 <conditional name="unknown_mass_shifts"> | |
161 <param name="how" type="select" label="Explaination for Unknown Mass Shifts"> | |
162 <option value="">None, disable delta mass interpretation by TagRecon</option> | |
163 <option value="blindptms">Blind PTMs</option> | |
164 <option value="mutations">Mutations</option> | |
165 <!-- TODO: Add preferredptms --> | |
166 </param> | |
167 <when value="blindptms"> | |
168 <!-- BlindPTMResidues ??? --> | |
169 </when> | |
170 <when value="mutations"> | |
171 <!-- BlosumScoreThreshold ??? BlosumThreshold ???--> | |
172 </when> | |
173 <when value="" /> | |
174 </conditional> | |
175 </inputs> | |
176 <!-- | |
177 Both: | |
178 AdjustPrecursorMass (defaults to false) | |
179 | |
180 TagRecon: | |
181 Skip for now: ComputeXCorr | |
182 Skip forever: ProteinSampleSize | |
183 | |
184 TO ADD: | |
185 | |
186 Both: Advanced, ClassSizeMultiplier, float 2.0. | |
187 --> | |
188 <outputs> | |
189 <data format="raw_pepxml" name="output" from_work_dir="output"> | |
190 <change_format> | |
191 <when input="output_type" value="mzid" format="mzid" /> | |
192 </change_format> | |
193 </data> | |
194 </outputs> | |
195 | |
196 <help> | |
197 **What it does** | |
198 | |
199 Performs protein identification via Directag and TagRecon. | |
200 </help> | |
201 </tool> | |
202 |