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author galaxyp
date Fri, 26 Sep 2014 14:52:07 -0400
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2:f8356c01939b 3:91fb73c8619c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool name="Peptide-Spectrum-Matches (PSMs) Evaluation" id="psm_eval" version="0.1.0"> 2 <tool name="Peptide-Spectrum-Matches (PSMs) Evaluator" id="psm_eval" version="0.1.0">
3 <requirements> 3 <requirements>
4 <requirement type="package">psm_eval</requirement> 4 <requirement type="package" version="22">binaries_for_psm_eval</requirement>
5 </requirements> 5 </requirements>
6 <description>Re-evalute potential PSMs using the psm-eval application.</description> 6 <description>Re-evalute potential PSMs using the psm-eval application.</description>
7 <command>psm_eval --settings $driver</command> 7 <command>psm_eval --settings $driver</command>
8 <configfiles> 8 <configfiles>
9 <configfile name="driver"># YAML driver for PSM Eval 9 <configfile name="driver"># YAML driver for PSM Eval
12 - path: $peak_list 12 - path: $peak_list
13 name: "$peak_list.display_name" 13 name: "$peak_list.display_name"
14 encoded_id: "${$__app__.security.encode_id( $peak_list.id )}|${$peak_list.extra_dir_file_name if hasattr($peak_list, 'extra_dir_file_name') else ''}" 14 encoded_id: "${$__app__.security.encode_id( $peak_list.id )}|${$peak_list.extra_dir_file_name if hasattr($peak_list, 'extra_dir_file_name') else ''}"
15 #end for 15 #end for
16 psms: $psms_cond.psms 16 psms: $psms_cond.psms
17 #set $psms_type = $psms_cond.type
18 #if $psms_type == "tpp_derived_report"
19 scan_id_column_index: ${int(str($psms_cond.scan_id_column)) - 1}
20 scan_source_column_index: ${int(str($psms_cond.scan_source_column)) - 1}
21 peptide_column_index: ${int(str($psms_cond.peptide_column)) - 1}
22 #end if
17 psms_type: $psms_cond.type 23 psms_type: $psms_cond.type
24
18 output: $output 25 output: $output
19 output_format: $output_type 26 output_format: $output_type
20 mass_type: $mass_type 27 mass_type: $mass_type
21 mass_tolerance: $default_mass_tolerance 28 mass_tolerance: $default_mass_tolerance
22 columns: 29 columns:
42 #end if 49 #end if
43 #if $peak_filter_type == 'quantile' 50 #if $peak_filter_type == 'quantile'
44 q: $peak_filter_options.q 51 q: $peak_filter_options.q
45 k: $peak_filter_options.k 52 k: $peak_filter_options.k
46 #end if 53 #end if
54 #if $peak_filter_type in ['mz_range_absolute', 'mz_range_percent_bp']
55 min: $peak_filter_options.min
56 max: $peak_filter_options.max
57 #end if
47 #end for 58 #end for
48 #end if 59 #end if
49 #if $type in ['ions_matched', 'peaks_matched'] 60 #if $type in ['ions_matched', 'peaks_matched']
50 ## Handle ions series 61 ## Handle ions series
51 #set $ions = $column_options 62 #set $ions = $column_options
64 #end for 75 #end for
65 </configfile> 76 </configfile>
66 </configfiles> 77 </configfiles>
67 <inputs> 78 <inputs>
68 <conditional name="psms_cond"> 79 <conditional name="psms_cond">
69 <param name="type" type="select" label="PSMs Type" help="ProteinPilot Peptide Report inputs results from ProteinPilot search algorithm. mzidentML inputs results from an open source search algorithm"> 80 <param name="type" type="select" label="PSMs Type" help="ProteinPilot Peptide Report inputs results are generated from the &quot;Convert ProteinPilot Group to Tabular&quot; tool. mzidentML inputs (beta) result from many search tools. Currently only MyriMatch has been tested, and with only one input file">
70 <option value="mzid">MzIdentML (mzid)</option> 81 <option value="mzid">MzIdentML (mzid)</option>
71 <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option> 82 <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option>
83 <option value="tpp_derived_report">Trans-Proteomic Pipeline Derived Peptide Report</option>
72 </param> 84 </param>
73 <when value="mzid"> 85 <when value="mzid">
74 <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="select appropriate file from history" /> 86 <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="select appropriate dataset from history" />
75 </when> 87 </when>
76 <when value="proteinpilot_peptide_report"> 88 <when value="proteinpilot_peptide_report">
77 <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="select appropriate file from history" /> 89 <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="select appropriate dataset from history" />
90 </when>
91 <when value="tpp_derived_report">
92 <param format="tabular" name="psms" type="data" label="Trans-Proteomic Pipeline Derived Peptide Report" help="select appropriate dataset from history" />
93 <param name="scan_source_column" label="Peak List Column" type="data_column" data_ref="psms" />
94 <param name="scan_id_column" label="Scan ID Column" type="data_column" data_ref="psms" />
95 <param name="peptide_column" label="Peptide Column" type="data_column" data_ref="psms" />
78 </when> 96 </when>
79 </conditional> 97 </conditional>
80 <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="select MZML file of experimental MS/MS data" /> 98 <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="select MZML dataset of experimental MS/MS scans" />
81 <param name="output_type" type="select" label="Output Type" help="Tabular is a spreadsheet containing columns of selected properties listed below. (select tabular as the output type and Peptide sequence as the column type. HTML provides visualization of matches (select HTML as the output type and ProtVis Link as the column type)"> 99 <param name="output_type" type="select" label="Output Type" help="Tabular is a spreadsheet containing columns of selected properties listed below. (select tabular as the output type and Peptide sequence as the column type. HTML provides visualization of matches (select HTML as the output type and ProtVis Link as the column type)">
82 <option value="tsv">Tabular (tsv)</option> 100 <option value="tsv">Tabular (tsv)</option>
83 <option value="html">HTML</option> 101 <option value="html">HTML</option>
84 </param> 102 </param>
85 <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" help="error of precursor ion (in Da). Recommended: 0.5 for LTQ/Orbitrap instrument; 0.01 for HCD/Orbitrap acquisition" /> 103 <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" help="error of fragment ion (in Da). Recommended: 0.5 for LTQ/Orbitrap instrument; 0.01 for HCD/Orbitrap acquisition" />
86 <param name="mass_type" type="select" label="Mass Type" help="Monoisotopic: selects most abundant isotopic MS peak for theoretical mass calculation. Average: uses average mass values for theoretical mass calculation"> 104 <param name="mass_type" type="select" label="Mass Type" help="Monoisotopic: selects most abundant isotopic MS peak for theoretical mass calculation. Average: uses average mass values for theoretical mass calculation. Average mass type is not well supported in this tool">
87 <option value="monoisotopic" selected="true">Monoisotopic</option> 105 <option value="monoisotopic" selected="true">Monoisotopic</option>
88 <option value="average">Average (has known problems)</option> 106 <option value="average">Average (has known problems)</option>
89 </param> 107 </param>
90 <repeat name="columns" title="Column"> 108 <repeat name="columns" title="Column">
91 <conditional name="column"> 109 <conditional name="column">
211 <conditional name="peak_filter"> 229 <conditional name="peak_filter">
212 <param type="select" label="Filter Peaks on" name="peak_filter_type"> 230 <param type="select" label="Filter Peaks on" name="peak_filter_type">
213 <option value="percent_tic">Intensity as a Percent of Total Ion Current</option> 231 <option value="percent_tic">Intensity as a Percent of Total Ion Current</option>
214 <option value="quantile">Intensity Quantile</option> 232 <option value="quantile">Intensity Quantile</option>
215 <option value="percent_max_intensity">Intensity as a Percent of Maximum Spectrum Peak Intensity</option> 233 <option value="percent_max_intensity">Intensity as a Percent of Maximum Spectrum Peak Intensity</option>
234 <option value="mz_range_absolute">m/z Range (absolute)</option>
235 <option value="mz_range_percent_bp">m/z Range (percent of base peak m/z)</option>
216 </param> 236 </param>
217 <when value="percent_tic"> 237 <when value="percent_tic">
218 <expand macro="percent_param" /> 238 <expand macro="percent_param" />
219 </when> 239 </when>
220 <when value="percent_max_intensity"> 240 <when value="percent_max_intensity">
221 <param name="percent" label="Percent of Maximum Peak Intensity" type="float" value="0.1" /> 241 <param name="percent" label="Percent of Maximum Peak Intensity" type="float" value="0.1" />
222 </when> 242 </when>
223 <when value="quantile"> 243 <when value="quantile">
224 <param name="q" label="q" type="integer" help="q is the number of partitions to break intensity into, k is the position to pull from. For instance if q=2 and k=1, the peaks above the median intensity will be used and if q=3 and k=2, the middle third of peaks by intensity will be used." value="2" /> 244 <param name="q" label="q" type="integer" help="q is the number of partitions to break intensity into, k is the position to pull from. For instance if q=2 and k=1, the peaks above the median intensity will be used and if q=3 and k=2, the middle third of peaks by intensity will be used." value="2" />
225 <param name="k" label="k" type="integer" value="1"/> 245 <param name="k" label="k" type="integer" value="1"/>
226 <expand macro="percent_param" /> 246 <expand macro="percent_param" />
227 </when> 247 </when>
248 <when value="mz_range_absolute">
249 <param name="min" label="Minimum m/z" type="float" help="" value="0.0" />
250 <param name="max" label="Maximum m/z" type="float" help="" value="100000.0" />
251 </when>
252 <when value="mz_range_percent_bp">
253 <param name="min" label="Minimum m/z (as percent of base peak m/z)" type="float" help="" value="0.0" />
254 <param name="max" label="Maximum m/z (as percent of base peak m/z)" type="float" help="" value="100000.0" />
255 </when>
228 </conditional> 256 </conditional>
229 <!-- TODO: Add m/z, intensity thresholds. --> 257 <!-- TODO: Add m/z, intensity thresholds. -->
230 </macro> 258 </macro>
231 <macro name="percent_param"> 259 <macro name="percent_param">
232 <param name="percent" label="Percent TIC Threshold" type="float" help="Filter all peaks whose intensity does not exceed this percent of total ion current." value="0.02" /> 260 <param name="percent" label="Percent TIC Threshold" type="float" help="Filter all peaks whose intensity does not exceed this percent of total ion current." value="0.02" />
233 </macro> 261 </macro>
234 </macros> 262 </macros>
235 <help> 263 <help>
236 **What it does** 264 **What it does**
237 265
238 Generates user-selected metrics in a tabular format for peptide-spectral matches using spectral/peptide summary generated from the search algorithm and mzml input files. The tabular format that is generated can be used for filtering based on user-defined thresholds. Alternatively, it can also provide visualization of peptide-spectral matches, thus allowing further metrics evaluation. 266 Generates user-selected metrics in a tabular format for peptide-spectral matches using spectral/peptide summary generated from a search tool and mzml input files. The tabular format that is generated can be used for filtering based on user-defined thresholds. Alternatively, it can also provide visualization of peptide-spectral matches, thus allowing further metrics evaluation.
239 <help> 267 </help>
240 </tool> 268 </tool>
241 269