# HG changeset patch
# User jmchilton
# Date 1368476174 14400
# Node ID d2c6b25e1a60877f9f82dfb92aaa1001baf64ea5
Initial commit.
diff -r 000000000000 -r d2c6b25e1a60 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Mon May 13 16:16:14 2013 -0400
@@ -0,0 +1,202 @@
+
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diff -r 000000000000 -r d2c6b25e1a60 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon May 13 16:16:14 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.
diff -r 000000000000 -r d2c6b25e1a60 README_GALAXYP.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md Mon May 13 16:16:14 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.
diff -r 000000000000 -r d2c6b25e1a60 README_REPO.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md Mon May 13 16:16:14 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).
+
+
diff -r 000000000000 -r d2c6b25e1a60 psm_eval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/psm_eval.xml Mon May 13 16:16:14 2013 -0400
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+
+
+
+ psm_eval
+
+ Re-evalute potential PSMs using the psm-eval application.
+ psm_eval --settings $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 $type == "link"
+ link_type: galaxy
+#end if
+#end for
+
+
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diff -r 000000000000 -r d2c6b25e1a60 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon May 13 16:16:14 2013 -0400
@@ -0,0 +1,14 @@
+
+
+
+
+
+ https://github.com/jmchilton/psm-eval/archive/8c05781330.zip
+ ./requirements.txt
+
+
+
+ Sets up a virtualenv for psm_eval.
+
+
+
\ No newline at end of file
diff -r 000000000000 -r d2c6b25e1a60 update.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh Mon May 13 16:16:14 2013 -0400
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$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