# HG changeset patch
# User iracooke
# Date 1432444362 14400
# Node ID 529ea20c1e6c63bc4688404eaf06effb1df3d2dd
# Parent aadf130415087811443817e6620ec0a74e70f0e0
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
diff -r aadf13041508 -r 529ea20c1e6c README
--- a/README Mon Jan 05 00:56:19 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML
-
-Requirements:
-This package uses protk and the trans_proteomic_pipeline. These must be installed separately.
-
-For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
\ No newline at end of file
diff -r aadf13041508 -r 529ea20c1e6c README.md
--- a/README.md Mon Jan 05 00:56:19 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-## What is it?
-Galaxy tool definition file and wrapper scripts for the [X!Tandem search engine](http://www.thegpm.org/tandem/index.html).
-
-## This tool requires that the protk rubygem and X!Tandem itself are installed.
-
-
diff -r aadf13041508 -r 529ea20c1e6c README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Sun May 24 01:12:42 2015 -0400
@@ -0,0 +1,39 @@
+X!Tandem
+========
+
+Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML
+
+Requirements
+------------
+
+This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work.
+
+.. _protk: https://github.com/iracooke/protk
+.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
+
+There are two ways you can satify these dependencies (choose one):
+
+1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_.
+
+2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed.
+
+.. _docker: https://www.docker.com/
+.. _here: https://github.com/iracooke/protk/#galaxy-integration
+.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
+__ container_
+
+
+Further Info
+------------
+
+The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__
+
+.. _github: https://github.com/iracooke/protk-galaxytools
+.. _issue: https://github.com/iracooke/protk-galaxytools/issues
+__ issue_
+
+
+Please visit the XTandem_ page on the GPM website for details of the search engine itself.
+
+.. _XTandem: http://www.thegpm.org/tandem/
+
diff -r aadf13041508 -r 529ea20c1e6c repository_dependencies.xml
--- a/repository_dependencies.xml Mon Jan 05 00:56:19 2015 -0500
+++ b/repository_dependencies.xml Sun May 24 01:12:42 2015 -0400
@@ -1,4 +1,4 @@
-
+
diff -r aadf13041508 -r 529ea20c1e6c tandem.xml
--- a/tandem.xml Mon Jan 05 00:56:19 2015 -0500
+++ b/tandem.xml Sun May 24 01:12:42 2015 -0400
@@ -1,194 +1,180 @@
-
-
+
+ Run an X!Tandem Search
- simonalpha/protk:1.4.0
- protk
-
-
- Run an X!Tandem Search
+ iracooke/protk-1.4.1
+ protk
+
+
+ #if $database.source_select=="built_in":
+ tandem_search.rb -d $database.dbkey
+ #else
+ tandem_search.rb -d $database.fasta_file
+ #end if
-
- #if $database.source_select=="built_in":
- tandem_search.rb -d $database.dbkey
- #else
- tandem_search.rb -d $database.fasta_file
- #end if
-
- #if $tandem_params.source_select=="built_in":
- -T $tandem_params.paramskey
- #else
- -T $tandem_params.params_file
- #end if
+ #if $tandem_params.source_select=="built_in":
+ -T $tandem_params.paramskey
+ #else
+ -T $tandem_params.params_file
+ #end if
- --var-mods='
- $variable_mods
- #for $custom_variable_mod in $custom_variable_mods:
- ,${custom_variable_mod.custom_mod}
- #end for
- '
+ --var-mods='
+ $variable_mods
+ #for $custom_variable_mod in $custom_variable_mods:
+ ,${custom_variable_mod.custom_mod}
+ #end for
+ '
- --fix-mods='
- $fixed_mods
- #for $custom_fix_mod in $custom_fix_mods:
- ,${custom_fix_mod.custom_mod}
- #end for
- '
-
- $input_file -o $output -r
-
- --enzyme=$enzyme
+ --fix-mods='
+ $fixed_mods
+ #for $custom_fix_mod in $custom_fix_mods:
+ ,${custom_fix_mod.custom_mod}
+ #end for
+ '
- --precursor-ion-tol-units=$precursor_tolu
-
- -v $missed_cleavages
+ $input_file -o $output -r
- -f $fragment_ion_tol
-
- -p $precursor_ion_tol
-
- $allow_multi_isotope_search
+ --enzyme=$enzyme
- $acetyl_protein_nterm
-
- $cleavage_semi
-
- $keep_spectra
-
- --threads $threads
-
-
+ --precursor-ion-tol-units=$precursor_tolu
+ -v $missed_cleavages
+ -f $fragment_ion_tol
+ -p $precursor_ion_tol
+ $allow_multi_isotope_search
+ $acetyl_protein_nterm
+ $cleavage_semi
+ $keep_spectra
+ --threads "\${GALAXY_SLOTS:-1}"
-
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**What it does**
diff -r aadf13041508 -r 529ea20c1e6c tandem_to_pepxml.xml
--- a/tandem_to_pepxml.xml Mon Jan 05 00:56:19 2015 -0500
+++ b/tandem_to_pepxml.xml Sun May 24 01:12:42 2015 -0400
@@ -1,26 +1,33 @@
-
-
- simonalpha/protk:1.4.0
- protk
- trans_proteomic_pipeline
-
+
+ Converts a tandem result file to pepXML
+
+ iracooke/protk-1.4.1
+ protk
+ trans_proteomic_pipeline
+
+
+ tandem_to_pepxml.rb $input_file -o $output
+
- Converts a tandem result file to pepXML
-
-
- tandem_to_pepxml.rb $input_file -o $output
-
+
+
+
-
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- Convert X!Tandem results to pepXML
-
-
+
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+
+ Convert X!Tandem results to pepXML
+
diff -r aadf13041508 -r 529ea20c1e6c test-data/tandem_to_pepxml_test.tandem
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tandem_to_pepxml_test.tandem Sun May 24 01:12:42 2015 -0400
@@ -0,0 +1,1145 @@
+
+
+
+
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+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
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+
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+
+
+
+
+tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1
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+
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+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
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+sp|O93590|ZAX_XENLA Homeobox protein zampogna OS=Xenopus laevis GN=zax PE=2 SV=1
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+sp|P22807|SLOU_DROME Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1
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+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
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+
+sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5
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+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
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+sp|P26797|HM19_CAEEL Homeobox protein ceh-19 OS=Caenorhabditis elegans GN=ceh-19 PE=2 SV=2
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+
+
+
+
+
+sp|O93367|TLX3_CHICK T-cell leukemia homeobox protein 3 OS=Gallus gallus GN=TLX3 PE=2 SV=1
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+
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+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
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+
+
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+
+
+
+
+
+
+
+sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+sp|P22711|TIN_DROME Muscle-specific homeobox protein tinman OS=Drosophila melanogaster GN=tin PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5
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+
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+
+
+
+
+sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
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+
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+
+
+
+
+
+
+
+
+tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1
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+
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+
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+
+
+
+sp|Q22909|HM30_CAEEL Homeobox protein ceh-30 OS=Caenorhabditis elegans GN=ceh-30 PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+sp|O93590|ZAX_XENLA Homeobox protein zampogna OS=Xenopus laevis GN=zax PE=2 SV=1
+
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+
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+tr|Q24786|Q24786_9METZ Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox1 PE=3 SV=1
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+tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
+
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+sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
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+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
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+sp|P22807|SLOU_DROME Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1
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+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
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+sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5
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+sp|Q01702|DLX3B_DANRE Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1
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+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
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+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
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+tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1
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+sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1
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+tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
+
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+tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2
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+tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2
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+
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+sp|Q22909|HM30_CAEEL Homeobox protein ceh-30 OS=Caenorhabditis elegans GN=ceh-30 PE=2 SV=2
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+sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
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+
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+tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
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+
+
+
+sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
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+tr|O97671|O97671_RABIT Homeobox protein (Fragment) OS=Oryctolagus cuniculus GN=HEX PE=2 SV=1
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+
+
+
+tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1
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+sp|P20269|HM05_CAEEL Homeobox protein ceh-5 OS=Caenorhabditis elegans GN=ceh-5 PE=2 SV=4
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+
+
+
+sp|P52955|LBX1_MOUSE Transcription factor LBX1 OS=Mus musculus GN=Lbx1 PE=1 SV=2
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+sp|P56407|HM09_CAEEL Homeobox protein ceh-9 OS=Caenorhabditis elegans GN=ceh-9 PE=4 SV=2
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+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
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+
+
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+
+
+
+
+
+
+sp|O08686|BARX2_MOUSE Homeobox protein BarH-like 2 OS=Mus musculus GN=Barx2 PE=2 SV=2
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+sp|P34663|HM23_CAEEL Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1
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+
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+sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1
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+
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+sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1
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+sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
+
+
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+
+
+
+
+
+
+
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+tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
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+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+
+sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5
+
+
+
+
+
+
+
+
+
+
+sp|P34663|HM23_CAEEL Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1
+
+
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+
+
+sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5
+
+
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+
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+
+
+
+
+tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+
+tr|Q23819|Q23819_HYDVD Cnox3 protein (Fragment) OS=Hydra viridissima GN=cnox3 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|Q23824|Q23824_HYDVD Msh protein (Fragment) OS=Hydra viridissima GN=msh PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|Q01702|DLX3B_DANRE Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+
+tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P34663|HM23_CAEEL Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5
+
+
+
+
+
+
+
+
+
+
+tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+
+tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+
+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+tr|Q23824|Q23824_HYDVD Msh protein (Fragment) OS=Hydra viridissima GN=msh PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+
+
+
+
+
+
+
+
+
+
+sp|P26797|HM19_CAEEL Homeobox protein ceh-19 OS=Caenorhabditis elegans GN=ceh-19 PE=2 SV=2
+
+
+
+
+
+
+
+
+
+
+ /Users/icooke/.rvm/gems/ruby-2.0.0-p353/gems/protk-1.2.6.pre6/lib/protk/data/tandem_isb_native_defaults.xml
+ /Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d_tandem.tandem.taxonomy.xml
+ 30
+ no
+
+ 0.1
+ 1234567890
+ no
+ yes
+ /Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d_tandem.tandem
+ no
+ yes
+ yes
+ all
+
+ no
+ spectrum
+ no
+ tandem-style.xsl
+
+
+
+
+ yes
+ [RK]|{P}
+ no
+
+ yes
+ AASequences.fasta
+ no
+ 0.1
+
+ yes
+
+ 15.994915@M
+
+ no
+ yes
+ no
+ no
+ no
+ 2
+ 4
+ no
+ yes
+ no
+ 100.0
+ monoisotopic
+ 0.4
+ Daltons
+ 5
+ 50.0
+ 600.0
+ 6
+ 100.0
+ 100.0
+ Daltons
+ no
+ /Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d.mgf
+ 1000
+ 1
+ 50
+ yes
+ no
+
+
+ yes
+
+ no
+
+
+
+
+ 10
+ no
+ no
+ no
+ 4000.0
+
+
+ /Users/icooke/Desktop/iptest/AASequences.fasta
+ no description
+ 0
+ 0
+ 528901
+ 33
+ 118
+ 2014:06:22:13:57:04
+ X! Tandem Sledgehammer (2013.09.01.1)
+ 6 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0.61
+ 0.0052
+ 0.00
+ 0.0000
+
+
diff -r aadf13041508 -r 529ea20c1e6c test-data/testdb.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testdb.fasta Sun May 24 01:12:42 2015 -0400
@@ -0,0 +1,38 @@
+>sp|ALBU_BOVIN|
+MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA
+FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK
+VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF
+KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC
+LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE
+FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE
+CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL
+GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL
+KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS
+RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC
+TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT
+ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV
+STQTALA
+>sp|AMYS_HUMAN|
+MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPK
+GFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTR
+CNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWD
+FNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNH
+LIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVI
+DLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWG
+FMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGF
+TRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCE
+HRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWT
+FSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAED
+PFIAIHAESKL
+>sp|CAS1_BOVIN|
+MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKE
+KVNELSKDIGSESTEDQAMEDIKQMEAESISSSEEIVPNSVEQKHIQKED
+VPSERYLGYLEQLLRLKKYKVPQLEIVPNSAEERLHSMKEGIHAQQKEPM
+IGVNQELAYFYPELFRQFYQLDAYPSGAWYYVPLGTQYTDAPSFSDIPNP
+IGSENSEKTTMPLW
+>sp|CAS2_BOVIN|
+MKFFIFTCLLAVALAKNTMEHVSSSEESIISQETYKQEKNMAINPSKENL
+CSTFCKEVVRNANEEEYSIGSSSEESAEVATEEVKITVDDKHYQKALNEI
+NQFYQKFPQYLQYLYQGPIVLNPWDQVKRNAVPITPTLNREQLSTSEENS
+KKTVDMESTEVFTKKTKLTEEEKNRLNFLKKISQRYQKFALPQYLKTVYQ
+HQKAMKPWIQPKTKVIPYVRYL
\ No newline at end of file
diff -r aadf13041508 -r 529ea20c1e6c test-data/tiny.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tiny.mzML Sun May 24 01:12:42 2015 -0400
@@ -0,0 +1,317 @@
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+ AAAAwB2Ok0A=
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+ AAAAYNaMjkAAAABAVAyPQAAAACCOYapA
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+ AAAA4B+Ok0A=
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diff -r aadf13041508 -r 529ea20c1e6c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun May 24 01:12:42 2015 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+