Mercurial > repos > galaxyp > psm_eval
changeset 0:77cc9cc99e15 draft
Initial commit.
| author | galaxyp |
|---|---|
| date | Fri, 10 May 2013 18:11:25 -0400 |
| parents | |
| children | 9743296a53a3 |
| files | LICENSE README.md README_GALAXYP.md README_REPO.md psm_eval.xml update.sh |
| diffstat | 6 files changed, 534 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 10 18:11:25 2013 -0400 @@ -0,0 +1,31 @@ +# Peptide-Spectrum Match Evaluator (psm_eval) + +This repository contains the psm_eval tool that allows for +re-evaulation of identified PSM based on multiple, flexiable user +supplied critiria and produces results that can be used to visualize +PSMs using ProtVis +(https://github.com/jmchilton/protvis/tree/lorikeet-reintegration). + + +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Fri May 10 18:11:25 2013 -0400 @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Fri May 10 18:11:25 2013 -0400 @@ -0,0 +1,9 @@ +# Peptide-Spectrum Match Evaluator (psm_eval) + +This repository contains the psm_eval tool that allows for +re-evaulation of identified PSM based on multiple, flexiable user +supplied critiria and produces results that can be used to visualize +PSMs using ProtVis +(https://github.com/jmchilton/protvis/tree/lorikeet-reintegration). + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/psm_eval.xml Fri May 10 18:11:25 2013 -0400 @@ -0,0 +1,235 @@ +<?xml version="1.0"?> +<tool name="Peptide-Spectrum-Matches (PSMs) Evaluation" id="psm_eval" version="0.1.0"> + <requirements> + <requirement type="package">psm_eval</requirement> + </requirements> + <description>Re-evalute potential PSMs using the psm-eval application.</description> + <command>psm_eval --settings $driver</command> + <configfiles> + <configfile name="driver"># YAML driver for PSM Eval +peak_lists: +#for $peak_list in $peak_lists: + - path: $peak_list + name: "$peak_list.display_name" + encoded_id: "${$__app__.security.encode_id( $peak_list.id )}" +#end for +psms: $psms_cond.psms +psms_type: $psms_cond.type +output: $output +output_format: $output_type +mass_type: $mass_type +mass_tolerance: $default_mass_tolerance +columns: +#for $column in $columns +#set $column_options = $column.column +#set $type = str(column_options['type']) + - type: ${type} +#if $type in ['ions_matched', 'peaks_matched'] + aggregate_by: $column_options.aggregate_by +#if $column_options.tolerance.specify + mass_tolerance: $column_options.tolerance.tolerance +#end if +#end if +#if $type in ['ions_matched', 'peaks_matched', 'num_peaks'] +## Handle peak filters + peak_filters: +#for $peak_filter in $column_options.peak_filters +#set $peak_filter_options = $peak_filter.peak_filter +#set $peak_filter_type = str(peak_filter_options['peak_filter_type']) + - type: $peak_filter_type +#if $peak_filter_type in ['percent_tic', 'quantile', 'percent_max_intensity'] + percent: $peak_filter_options.percent +#end if +#if $peak_filter_type == 'quantile' + q: $peak_filter_options.q + k: $peak_filter_options.k +#end if +#end for +#end if +#if $type in ['ions_matched', 'peaks_matched'] +## Handle ions series +#set $ions = $column_options + ions: + series: $ions.ion_series +#if $ions.losses + losses: $ions.losses +#end if +#end if +#if $type == "source_statistic" + statistic_name: ${str(column_options['source_statistic'])} +#end if +#if $type == "link" + link_type: galaxy +#end if +#end for + </configfile> + </configfiles> + <inputs> + <conditional name="psms_cond"> + <param name="type" type="select" label="PSMs Type" help=""> + <option value="mzid">MzIdentML (mzid)</option> + <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option> + </param> + <when value="mzid"> + <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="" /> + </when> + <when value="proteinpilot_peptide_report"> + <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="" /> + </when> + </conditional> + <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="" /> + <param name="output_type" type="select" label="Output Type" help=""> + <option value="tsv">Tabular (tsv)</option> + <option value="html">HTML</option> + </param> + <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" /> + <param name="mass_type" type="select" label="Mass Type"> + <option value="monoisotopic" selected="true">Monoisotopic</option> + <option value="average">Average (has known problems)</option> + </param> + <repeat name="columns" title="Column"> + <conditional name="column"> + <param type="select" name="type" label="Column Type"> + <option value="peptide">Peptide Sequence</option> + <option value="scan_index">Scan Index</option> + <option value="scan_number">Scan Number</option> + <option value="scan_id">Scan ID</option> + <option value="scan_source">Peak List</option> + <option value="num_peaks">Number of Peaks</option> + <option value="peaks_matched">Peaks Matched Statistic</option> + <option value="ions_matched">Ions Matched Statistic</option> + <option value="total_ion_current">Total Ion Current</option> + <option value="source_statistic">Statistic from PSM Source</option> + <option value="link">ProtVis Link</option> + </param> + <when value="num_peaks"> + <expand macro="peak_filters" /> + </when> + <when value="peaks_matched"> + <param name="aggregate_by" label="Peak Matching Statistic" type="select"> + <option value="count">Number of Matched Peaks</option> + <option value="count_missed">Number of Unmatched Peaks</option> + <option value="percent">Percent of Matched Peaks</option> + <option value="percent_missed">Percent of Unmatched Peaks</option> + </param> + <expand macro="ions" /> + <expand macro="peak_filters" /> + <expand macro="tolerance_conditional" /> + </when> + <when value="ions_matched"> + <param name="aggregate_by" label="Ion Matching Statistic" type="select"> + <option value="count">Number of Matched Ions</option> + <option value="count_missed">Number of Unmatched Ions</option> + <option value="count_longest_stretch">Longest Stretch of Matched Ions</option> + <option value="percent">Percent of Matched Ions</option> + <option value="percent_missed">Percent of Unmatched Ions</option> + <option value="list_matches">List Matched Ions</option> + <option value="list_misses">List Unmatched Ions</option> + </param> + <expand macro="ions" /> + <expand macro="peak_filters" /> + <expand macro="tolerance_conditional" /> + </when> + <when value="source_statistic"> + <param name="source_statistic" label="PSM Source Statistic" type="select"> + <option value="xcorr">xcorr</option> + <option value="MyriMatch:MVH">MyriMatch: MVH</option> + <option value="MyriMatch:mzFidelity">MyriMatch: mzFidelity</option> + <option value="Conf">Conf</option> + </param> + </when> + <when value="link"> + </when> + </conditional> + </repeat> + </inputs> + <outputs> + <data format="tabular" name="output" label="PSM Evaluation of ${on_string}"> + <change_format> + <when input="output_type" value="html" format="html" /> + </change_format> + </data> + </outputs> + <macros> + <macro name="ions"> + <param name="ion_series" type="select" multiple="true" label="Ion Series"> + <option value="a1">a1</option> + <option value="a2">a2</option> + <option value="a3">a3</option> + <option value="b1">b1</option> + <option value="b2">b2</option> + <option value="b3">b3</option> + <option value="c1">c1</option> + <option value="c2">c2</option> + <option value="c3">c3</option> + <option value="x1">x1</option> + <option value="x2">x2</option> + <option value="x3">x3</option> + <option value="y1">y1</option> + <option value="y2">y2</option> + <option value="y3">y3</option> + <option value="z1">z1</option> + <option value="z2">z2</option> + <option value="z3">z3</option> + <option value="m1">M1</option> + <option value="m2">M2</option> + <option value="internal">Internal Ions</option> + </param> + <param name="losses" type="select" multiple="true" label="Losses" value=""> + <option value="H2O">H2O</option> + <option value="NH3">NH3</option> + <option value="CO">CO (-28) on internal ions</option> + </param> + </macro> + <macro name="tolerance_conditional"> + <conditional name="tolerance"> + <param name="specify" label="Specify Mass Tolerance" type="boolean" /> + <when value="false"> + </when> + <when value="true"> + <param name="tolerance" value="0.5" label="Tolerance" type="float" /> + </when> + </conditional> + </macro> + <!-- + <macro name="conditional_ions"> + <conditional name="specify_ions"> + <param type="boolean" truevalue="true" falsevalue="false" name="specify" label="Specify Ions?" /> + <when value="true"> + <expand macro="ions" /> + </when> + <when value="false" /> + </conditional> + </macro> + --> + <macro name="peak_filters"> + <repeat name="peak_filters" title="Peak Filter"> + <expand macro="peak_filter" /> + </repeat> + </macro> + <macro name="peak_filter"> + <conditional name="peak_filter"> + <param type="select" label="Filter Peaks on" name="peak_filter_type"> + <option value="percent_tic">Intensity as a Percent of Total Ion Current</option> + <option value="quantile">Intensity Quantile</option> + <option value="percent_max_intensity">Intensity as a Percent of Maximum Spectrum Peak Intensity</option> + </param> + <when value="percent_tic"> + <expand macro="percent_param" /> + </when> + <when value="percent_max_intensity"> + <param name="percent" label="Percent of Maximum Peak Intensity" type="float" value="0.1" /> + </when> + <when value="quantile"> + <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" /> + <param name="k" label="k" type="integer" value="1"/> + <expand macro="percent_param" /> + </when> + </conditional> + <!-- TODO: Add m/z, intensity thresholds. --> + </macro> + <macro name="percent_param"> + <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" /> + </macro> + </macros> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Fri May 10 18:11:25 2013 -0400 @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi