# HG changeset patch
# User iracooke
# Date 1418615992 18000
# Node ID 558fdcf3b617eb9b8ebf0c0d5a6bec356b256c93
# Parent  189820586caf0ff35789205b8e6fa464e5bbb007
Deleted selected files

diff -r 189820586caf -r 558fdcf3b617 macros.xml
--- a/macros.xml	Sun Dec 14 22:59:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.35">peptide_shaker</requirement>
-            <requirement type="package" version="1.23">searchgui</requirement>
-        </requirements>
-    </xml>
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" level="fatal" description="Job Failed" />
-            <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
-            <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
-        </stdio>
-    </xml>
-    <token name="@GENERAL_PARAMETERS@">
-            -frag_tol "${fragment_tol}"
-            -prec_tol "${precursor_ion_tol}"
-            -prec_ppm "${precursor_ion_tol_units}"
-            -enzyme "${enzyme}"
-            #set $fixed_mods_str = $fixed_modifications or ''
-            #set $variable_mods_str = $variable_modifications or ''
-            #if $fixed_mods_str
-                -fixed_mods "$fixed_mods_str" 
-            #end if
-            #if $variable_mods_str
-                -variable_mods "$variable_mods_str"
-            #end if
-            -min_charge $min_charge
-            -max_charge $max_charge
-            -mc $missed_cleavages
-            -fi $forward_ion
-            -ri $reverse_ion
-    </token>
-
-    <xml name="general_options">
-        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
-            help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
-            <option value="1">Parts per million (ppm)</option>
-            <option value="0">Daltons</option>
-        </param>
-        <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
-            help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
-        <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
-            help="Provide error value for fragment ions, based on instrument used"/>
-        <param name="enzyme" type="select" label="Enzyme"
-            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
-            <option value="Trypsin">Trypsin</option>
-            <option value="Arg-C">Arg-C</option>
-            <option value="CNBr">CNBr</option>
-            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
-            <option value="Formic Acid">Formic Acid</option>
-            <option value="Lys-C">Lys-C</option>
-            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
-            <option value="Pepsin A">Pepsin A</option>
-            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
-            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
-            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-            <option value="whole protein">whole protein</option>
-            <option value="Asp-N">Asp-N</option>
-            <option value="Glu-C">Glu-C</option>
-            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
-            <option value="Top-Down">Top-Down</option>
-            <option value="Semi-Tryptic">Semi-Tryptic</option>
-            <option value="No enzyme">No enzyme</option>
-            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
-            <option value="Asp-N (DE)">Asp-N (DE)</option>
-            <option value="Glu-C (DE)">Glu-C (DE)</option>
-            <option value="Lys-N (K)">Lys-N (K)</option>
-            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
-            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
-            <option value="Semi-Glu-C">Semi-Glu-C</option>
-        </param>
-        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
-            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
-        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
-            help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
-            <options from_file="searchgui_mods.loc">
-                <column name="name" index="0" />
-                <column name="value" index="0" />
-            </options>
-        </param>
-        <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 
-            help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
-            <options from_file="searchgui_mods.loc">
-                <column name="name" index="0" />
-                <column name="value" index="0" />
-            </options>
-        </param>
-        <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
-        <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
-        <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
-            <option value="a">a</option>
-            <option value="b" selected="true">b</option>
-            <option value="c">c</option>
-        </param>
-        <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
-            <option value="x">x</option>
-            <option value="y" selected="true">y</option>
-            <option value="z">z</option>
-        </param>
-    </xml>
-
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1186/1471-2105-12-70</citation>
-            <citation type="doi">10.1002/pmic.201000595</citation>
-        </citations>
-    </xml>
-
-</macros>
diff -r 189820586caf -r 558fdcf3b617 searchgui.xml
--- a/searchgui.xml	Sun Dec 14 22:59:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,343 +0,0 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.23.0">
-    <description>
-        Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
-    </description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #from datetime import datetime
-        #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
-        #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
-        #set $temp_stderr = 'macs2_stderr'
-
-        mkdir output;
-        mkdir output_reports;
-        cwd=`pwd`;
-        #for $mgf in $peak_lists:
-            #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
-            ln -s '${mgf}' '${input_name}';
-        #end for
-        ##ln -s "${input_database}" input_database.fasta;
-        cp "${input_database}" input_database.fasta;
-
-        ###########################################
-        ####       Creating decoy database     ####
-        ###########################################
-        #if $create_decoy:
-            echo "Creating decoy database.";
-            java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;
-            rm input_database.fasta;
-            cp input_database_concatenated_target_decoy.fasta input_database.fasta;
-            ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
-        #end if
-
-        #####################################################
-        ## generate IdentificationParameters for SearchGUI ##
-        #####################################################
-
-        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
-            -out SEARCHGUI_IdentificationParameters.parameters
-
-            @GENERAL_PARAMETERS@
-
-            -db input_database.fasta
-
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
-
-                    -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
-                    -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
-                    -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
-                    -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
-                    -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
-
-                    #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
-                        -xtandem_refine 1
-                        -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
-                        -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
-                        -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
-                        -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
-                        -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
-                    #end if
-                #end if
-
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa_hitlist_length ${advanced.omssa.hitlist_length}
-                    -omssa_remove_prec ${advanced.omssa.remove_precursor}
-                    -omssa_scale_prec ${advanced.omssa.scale_precursor}
-                    -omssa_estimate_charge ${advanced.omssa.estimate_charge}
-                #end if
-
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf_decoy ${advanced.msgf.msgf_decoy}
-                    -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
-                    -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
-                    -msgf_termini ${advanced.msgf.msgf_termini}
-                    -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
-                #end if
-
-                ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                ##end if
-
-            #end if
-
-        2> $temp_stderr)
-        &&
-
-        ################
-        ## Search CLI ##
-        ################
-        (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 
-            -temp_folder `pwd`
-            -spectrum_files \$cwd
-            -output_folder \$cwd/output
-            -id_params SEARCHGUI_IdentificationParameters.parameters
-
-            -threads "\${GALAXY_SLOTS:-12}"
-            -correct_titles "${correct_titles}"
-            $missing_titles
-            -mgf_splitting "${mgf_splitting}"
-            -mgf_spectrum_count "${mgf_spectrum_count}"
-
-            ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
-            ## the tree is generated afterwards in PeptideShaker
-            -protein_index 0
-
-            ##-makeblastdb_folder \$BLAST_ROOT_DIR
-
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
-                    -xtandem 1
-                #else
-                    -xtandem 0
-                #end if
-
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa 1
-                #else
-                    -omssa 0
-                #end if
-
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf 1
-                #else
-                    -msgf 0
-                #end if
-
-                #if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                    -ms_amanda 1
-                #else
-                    -ms_amanda 0
-                #end if
-
-                #if $advanced.myrimatch.myrimatch_selector == "yes"
-                    -myrimatch 1
-                #else
-                    -myrimatch 0
-                #end if
-
-                #if $advanced.comet.comet_selector == "yes"
-                    -comet 1
-                #else
-                    -comet 0
-                #end if
-
-            #else
-                -ms_amanda 0
-            #end if
-            
-            ## single zip file
-            -output_option 0
-
-        2>> $temp_stderr)
-
-        &&
-
-        exit_code_for_galaxy=\$?;
-        cat $temp_stderr 2&gt;&amp;1;
-        (exit \$exit_code_for_galaxy)
-]]>
-    </command>
-    <inputs>
-        <param format="fasta" name="input_database" type="data" label="Protein Database"
-            help="Select FASTA database from history"/>
-
-        <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
-            label="Create a concatenated target/decoy database before running PeptideShaker"
-            help="Selecting this option will help PeptideShaker calculate FDR values" />
-
-        <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
-            help="Select appropriate MGF dataset(s) from history" />
-
-        <expand macro="general_options"/>
-
-        <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
-            help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
-            <option value="0">no correction</option>
-            <option value="1" selected="True">rename spectra</option>
-            <option value="2">delete spectra</option>
-        </param>
-
-        <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
-            label="Add missing spectrum titles" help="(-missing_titles)"/>
-
-        <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
-            help="Choose a smaller value if you are running on a machine with limited memory"/>
-
-        <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
-            help="Choose a smaller value if you are running on a machine with limited memory"/>
-
-        <conditional name="advanced">
-            <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
-                <option value="basic" selected="True">Basic</option>
-                <option value="advanced">Advanced</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <conditional name="xtandem">
-                    <param name="xtandem_selector" type="select" label="Run X!Tandem search">
-                        <option value="yes" selected="True">Search with X!Tandem</option>
-                        <option value="no">No X!Tandem search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
-                        <param name="xtandem_min_peaks" type="integer" value="15" 
-                            label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
-                        <param name="xtandem_min_frag_mz" type="integer" value="200" 
-                            label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
-                        <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-                        <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
-
-                        <conditional name="xtandem_refine"><!-- -xtandem_refine -->
-                            <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
-                                <option value="no" selected="True">Don't refine</option>
-                                <option value="yes" >Use refinement</option>
-                            </param>
-                            <when value="no"/>
-                            <when value="yes">
-                                <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0"
-                                    label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
-                                <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
-                                <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
-                                <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
-                                <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
-                            </when>
-                        </conditional>
-                    </when>
-                </conditional>
-
-                <conditional name="omssa">
-                    <param name="omssa_selector" type="select" label="Run OMSSA search">
-                        <option value="yes" selected="True">Search with OMSSA</option>
-                        <option value="no">No OMSSA search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
-                        <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-                        <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
-                        <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    </when>
-                </conditional>
-
-                <conditional name="msgf">
-                    <param name="msgf_selector" type="select" label="Run MSGF search">
-                        <option value="yes" selected="True">Search with MSGF</option>
-                        <option value="no">No MSGF search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0"
-                            label="Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
-                        <param name="msgf_min_pep_length" type="integer" value="6"
-                            label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
-                        <param name="msgf_max_pep_length" type="integer" value="30" 
-                            label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
-                        <param name="msgf_termini" type="select" format="text" 
-                            label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
-                            <option value="0">0 (ie non-specific cleavage)</option>
-                            <option value="1">1 (ie semi-tryptic cleavage)</option>
-                            <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
-                        </param>
-                        <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
-                    </when>
-                </conditional>
-
-                <conditional name="ms_amanda">
-                    <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
-                        <option value="yes">Search with MS Amanda</option>
-                        <option value="no" selected="True">No MS Amanda search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-
-                <conditional name="myrimatch">
-                    <param name="myrimatch_selector" type="select" label="Run MyriMatch search">
-                        <option value="yes">Search with MyriMatch</option>
-                        <option value="no" selected="True">No MyriMatch search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-
-                <conditional name="comet">
-                    <param name="comet_selector" type="select" label="Run Comet search">
-                        <option value="yes">Search with Comet</option>
-                        <option value="no" selected="True">No Comet search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-
-            </when>
-        </conditional>
-
-    </inputs>
-    <outputs>
-        <data format="bgzip" name="searchgui_results" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_database" value="tinydb.fasta"/>
-            <param name="peak_lists" value="tinyspectra.mgf"/>
-            <param name="precursor_ion_tol" value="100"/>
-            <param name="fixed_modifications" value="carbamidomethyl c"/>
-            <param name="variable_modifications" value="oxidation of m"/>
-            <param name="min_charge" value="1"/>
-            <param name="max_charge" value="3"/>
-            <param name="advanced_type_selector" value="advanced"/>
-            <!--param name="xtandem_selector" value="no"/>-->
-            <param name="xtandem_selector" value="yes"/>
-            <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
-
-            <param name="omssa_selector" value="no"/>
-            <param name="msgf_selector" value="yes"/>
-            <param name="ms_amanda_selector" value="no"/>
-            
-            <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> 
-        </test>
-    </tests>
-    <help>
-**What it does**
-
-Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI.
-
-
-    </help>
-    <expand macro="citations" />
-</tool>
diff -r 189820586caf -r 558fdcf3b617 test-data/._tinyoutput.cps
Binary file test-data/._tinyoutput.cps has changed
diff -r 189820586caf -r 558fdcf3b617 test-data/tinydb.fasta
--- a/test-data/tinydb.fasta	Sun Dec 14 22:59:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
->cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68
-LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV
->cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14
-DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ
->cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32
-KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR
->cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67
-METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
->cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67
-METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
->cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10
-SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
->cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20
-YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL
->cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91
-MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
->cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92
-MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
->cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0
-MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ
->cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87
-MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN
->cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16
-FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
diff -r 189820586caf -r 558fdcf3b617 test-data/tinyoutput.cps
Binary file test-data/tinyoutput.cps has changed
diff -r 189820586caf -r 558fdcf3b617 test-data/tinyspectra.mgf
--- a/test-data/tinyspectra.mgf	Sun Dec 14 22:59:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6153 +0,0 @@
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-END IONS
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-BEGIN IONS
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-END IONS
-
-BEGIN IONS
-TITLE= Cmpd 591, +MSn(509.9328), 63.7 min
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-END IONS
-
-BEGIN IONS
-TITLE= Cmpd 204, +MSn(524.2825), 35.5 min
-PEPMASS=524.28252	121118
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-1118.57910	362	
-END IONS
-