# HG changeset patch
# User galaxyp
# Date 1521571184 14400
# Node ID f01f84cbd265d52187c991fffd8b330dc07f2f8c
# Parent  d55a7181895c5182327d7d8294f6b046d923ab38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

diff -r d55a7181895c -r f01f84cbd265 readme.md
--- a/readme.md	Mon Feb 12 12:55:30 2018 -0500
+++ b/readme.md	Tue Mar 20 14:39:44 2018 -0400
@@ -170,16 +170,6 @@
     </tests>
     ```
     
-
- * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
-   by the automatic conversion step and are therefore in `tools_blacklist.txt`:
-    * SeedListGenerator
-    * SpecLibSearcher
-    * MapAlignerIdentification
-    * MapAlignerPoseClustering
-    * MapAlignerSpectrum
-    * MapAlignerRTTransformer
-    
  * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
     * OMSSAAdapter
     * MyrimatchAdapter
diff -r d55a7181895c -r f01f84cbd265 test-data/FileFilter_1_input.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FileFilter_1_input.mzML	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,336 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+	<cvList count="2">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+		</fileContent>
+		<contact>
+			<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />
+			<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />
+		</contact>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
+			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0"  unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
+		</sample>
+	</sampleList>
+	<softwareList count="12">
+		<software id="so_in_0" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_default" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_dp_sp_0_pm_0" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_dp_sp_0_pm_1" version="version_string" >
+			<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />
+		</software>
+	</softwareList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="ic_0">
+			<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+			<componentList count="3">
+				<source order="0">
+					<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />
+				</source>
+				<analyzer order="0">
+					<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />
+				</analyzer>
+				<detector order="0">
+					<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />
+				</detector>
+			</componentList>
+			<softwareRef ref="so_in_0" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="10">
+		<dataProcessing id="dp_sp_0">
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
+				<cvParam cvRef="MS" accession="MS:1000543" name="data processing action" />
+			</processingMethod>
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
+				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="1999-12-31+23:59" />
+				<userParam name="parameter: mode" type="xsd:string" value="test_mode"/>
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0">
+		<spectrumList count="10" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="spectrum=1" index="0" defaultArrayLength="787" dataProcessingRef="dp_sp_0">
+				<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan>
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="20.8713" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="8396">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
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+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
diff -r d55a7181895c -r f01f84cbd265 test-data/MetaProSIP_1_input.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MetaProSIP_1_input.fasta	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,6 @@
+>contig23640_802236  length=2326  numreads=28 strand:-1 frame:0 orf_location:136:990
+GGIPNEENWNFGSSDGSGLPVRGSGQRRDVLGRLCRRNFTSSIGQSVNVRDVEASGFAGG
+MSRYHFKYGGAVDPTVLGGVKLGTWFVKEGFAGWSGYPDWCKYFGFYTDFSYHRFYTRDN
+RISGTDFFAAYGGGSAALGDVGFMKTEGMVATWAFMLAARYGFFQDSEVPFGRLQPYVAV
+GPAIMFSSMKPKIWTQFNEPNVGFPNPDLVYSPGNQSSTDLGLAVDTGIRYMCLKNVSLD
+ISFKYRYAQPHYNFSGQDGSVMVPAHMSLSPALNLYSFQAGVAYHF
diff -r d55a7181895c -r f01f84cbd265 test-data/MetaProSIP_1_input.featureXML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MetaProSIP_1_input.featureXML	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<featureMap version="1.9" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+	<dataProcessing completion_time="2017-12-08T12:44:40">
+		<software name="FileFilter" version="2.3.0" />
+		<processingAction name="Data filtering" />
+		<UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>
+		<UserParam type="string" name="parameter: in_type" value=""/>
+		<UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>
+		<UserParam type="string" name="parameter: out_type" value=""/>
+		<UserParam type="string" name="parameter: rt" value=":"/>
+		<UserParam type="string" name="parameter: mz" value=":"/>
+		<UserParam type="string" name="parameter: int" value=":"/>
+		<UserParam type="string" name="parameter: sort" value="false"/>
+		<UserParam type="string" name="parameter: log" value=""/>
+		<UserParam type="int" name="parameter: debug" value="0"/>
+		<UserParam type="int" name="parameter: threads" value="1"/>
+		<UserParam type="string" name="parameter: no_progress" value="false"/>
+		<UserParam type="string" name="parameter: force" value="false"/>
+		<UserParam type="string" name="parameter: test" value="false"/>
+		<UserParam type="float" name="parameter: peak_options:sn" value="0"/>
+		<UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>
+		<UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>
+		<UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>
+		<UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>
+		<UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>
+		<UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/>
+		<UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/>
+		<UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/>
+		<UserParam type="string" name="parameter: peak_options:int_precision" value="32"/>
+		<UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/>
+		<UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/>
+		<UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/>
+		<UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/>
+		<UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/>
+		<UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/>
+		<UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/>
+		<UserParam type="string" name="parameter: spectra:remove_mode" value=""/>
+		<UserParam type="string" name="parameter: spectra:remove_activation" value=""/>
+		<UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>
+		<UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>
+		<UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>
+		<UserParam type="string" name="parameter: spectra:select_mode" value=""/>
+		<UserParam type="string" name="parameter: spectra:select_activation" value=""/>
+		<UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>
+		<UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>
+		<UserParam type="string" name="parameter: spectra:select_polarity" value=""/>
+		<UserParam type="string" name="parameter: feature:q" value=":"/>
+		<UserParam type="intList" name="parameter: consensus:map" value="[]"/>
+		<UserParam type="string" name="parameter: consensus:map_and" value="false"/>
+		<UserParam type="string" name="parameter: consensus:blackorwhitelist:blacklist" value="true"/>
+		<UserParam type="string" name="parameter: consensus:blackorwhitelist:file" value=""/>
+		<UserParam type="intList" name="parameter: consensus:blackorwhitelist:maps" value="[]"/>
+		<UserParam type="float" name="parameter: consensus:blackorwhitelist:rt" value="60"/>
+		<UserParam type="float" name="parameter: consensus:blackorwhitelist:mz" value="0.01"/>
+		<UserParam type="string" name="parameter: consensus:blackorwhitelist:use_ppm_tolerance" value="false"/>
+		<UserParam type="string" name="parameter: f_and_c:charge" value=":"/>
+		<UserParam type="string" name="parameter: f_and_c:size" value=":"/>
+		<UserParam type="stringList" name="parameter: f_and_c:remove_meta" value="[]"/>
+		<UserParam type="string" name="parameter: id:remove_clashes" value="false"/>
+		<UserParam type="string" name="parameter: id:keep_best_score_id" value="false"/>
+		<UserParam type="stringList" name="parameter: id:sequences_whitelist" value="[]"/>
+		<UserParam type="stringList" name="parameter: id:accessions_whitelist" value="[]"/>
+		<UserParam type="string" name="parameter: id:remove_annotated_features" value="false"/>
+		<UserParam type="string" name="parameter: id:remove_unannotated_features" value="true"/>
+		<UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>
+		<UserParam type="string" name="parameter: id:blacklist" value=""/>
+		<UserParam type="float" name="parameter: id:rt" value="0.1"/>
+		<UserParam type="float" name="parameter: id:mz" value="0.001"/>
+		<UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>
+		<UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>
+		<UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>
+		<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>
+		<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/>
+		<UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/>
+		<UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/>
+		<UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/>
+		<UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/>
+		<UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/>
+	</dataProcessing>
+	<IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8">
+		<SearchParameters db="/raid/sachsenb/Jana/fasta/Zeitz_1and2_454AllContigs_HEX.fasta.psq" db_version="" taxonomy="0" mass_type="monoisotopic" charges="+2-+3" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0.5" peak_mass_tolerance_ppm="false" >
+			<FixedModification name="Carbamidomethyl (C)" />
+			<VariableModification name="Oxidation (M)" />
+		</SearchParameters>
+		<ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0">
+			<ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence="">
+			</ProteinHit>
+		</ProteinIdentification>
+	</IdentificationRun>
+	<featureList count="1">
+		<feature id="f_988449706551050085">
+			<position dim="0">4831.43346884947</position>
+			<position dim="1">666.862287171363</position>
+			<intensity>3.25608e+06</intensity>
+			<quality dim="0">0</quality>
+			<quality dim="1">0</quality>
+			<overallquality>0.882314</overallquality>
+			<charge>2</charge>
+			<convexhull nr="0">
+				<pt x="4803.8473" y="666.862043575291" />
+				<pt x="4805.8211" y="666.862135109963" />
+			</convexhull>
+			<convexhull nr="1">
+				<pt x="4803.8473" y="667.364150217852" />
+				<pt x="4805.8211" y="667.363529666672" />
+			</convexhull>
+			<convexhull nr="2">
+				<pt x="4805.8211" y="667.865608520739" />
+				<pt x="4807.3928" y="667.864992849711" />
+			</convexhull>
+			<convexhull nr="3">
+				<pt x="4810.5312" y="668.364801015548" />
+				<pt x="4812.1021" y="668.365292284748" />
+			</convexhull>
+			<PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" >
+				<PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0">
+					<UserParam type="string" name="target_decoy" value="target"/>
+					<UserParam type="string" name="protein_references" value="unique"/>
+				</PeptideHit>
+			</PeptideIdentification>
+			<UserParam type="int" name="label" value="453"/>
+			<UserParam type="float" name="score_fit" value="0.783165906030983"/>
+			<UserParam type="float" name="score_correlation" value="0.994014816652796"/>
+			<UserParam type="float" name="FWHM" value="23.5379981994629"/>
+			<UserParam type="int" name="spectrum_index" value="1569"/>
+			<UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/>
+		</feature>
+	</featureList>
+</featureMap>
diff -r d55a7181895c -r f01f84cbd265 test-data/MetaProSIP_1_input.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MetaProSIP_1_input.mzML	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,2621 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+	<cvList count="5">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
+		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
+		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+		</fileContent>
+		<sourceFileList count="1">
+			<sourceFile id="sf_ru_0" name="Zeitz_SIP_13-II_020_picked.mzML" location="file:///nfs/wsi/abi/old-data/sachsenb/OpenMS_IDE/MetaProSIP/Zeitz">
+				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="cda64713a3466f7bf74af2a42da97351aaff691b" />
+				<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />
+				<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
+			</sourceFile>
+		</sourceFileList>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
+			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
+		</sample>
+	</sampleList>
+	<softwareList count="5">
+		<software id="so_in_0" version="2.5.5" >
+			<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
+		</software>
+		<software id="so_default" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_dp_sp_0_pm_0" version="2.0.1885" >
+			<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" />
+		</software>
+		<software id="so_dp_sp_0_pm_1" version="1.8.0" >
+			<cvParam cvRef="MS" accession="MS:1000763" name="PeakPicker" />
+		</software>
+		<software id="so_dp_sp_0_pm_2" version="2.3.0" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />
+		</software>
+	</softwareList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="ic_0">
+			<cvParam cvRef="MS" accession="MS:1000556" name="LTQ Orbitrap XL" />
+			<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN01757B"/>
+			<componentList count="3">
+				<source order="1">
+					<cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" />
+					<cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" />
+				</source>
+				<analyzer order="2">
+					<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
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+					<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" />
+				</analyzer>
+				<detector order="3">
+					<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" />
+				</detector>
+			</componentList>
+			<softwareRef ref="so_in_0" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="dp_sp_0">
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
+			</processingMethod>
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
+				<cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
+				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-03-10+11:54" />
+				<userParam name="parameter: no_progress" type="xsd:string" value="true"/>
+				<userParam name="parameter: type" type="xsd:string" value="high_res"/>
+				<userParam name="parameter: in" type="xsd:string" value="mzML/Zeitz_SIP_13-II_020.mzML"/>
+				<userParam name="parameter: out" type="xsd:string" value="/tmp/TOPPAS_tmp/signal_processing/002_PeakPicker_high_res/out/Zeitz_SIP_13-II_020.mzML_tmp1"/>
+				<userParam name="parameter: ini" type="xsd:string" value="/tmp/TOPPAS_tmp/signal_processing/002_PeakPicker_high_res/PeakPicker_high_res.ini1"/>
+				<userParam name="parameter: log" type="xsd:string" value=""/>
+				<userParam name="parameter: debug" type="xsd:integer" value="0"/>
+				<userParam name="parameter: threads" type="xsd:integer" value="1"/>
+				<userParam name="parameter: test" type="xsd:string" value="false"/>
+				<userParam name="parameter: algorithm:signal_to_noise" type="xsd:double" value="1"/>
+				<userParam name="parameter: algorithm:ms1_only" type="xsd:string" value="true"/>
+			</processingMethod>
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_2">
+				<cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
+				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2017-12-08+12:43" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" startTimeStamp="2010-09-30T09:34:23" defaultSourceFileRef="sf_ru_0">
+		<userParam name="mzml_id" type="xsd:string" value="Zeitz_SIP_13-II_020"/>
+		<spectrumList count="57" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="controllerType=0 controllerNumber=1 scan=6048" index="0" defaultArrayLength="24" dataProcessingRef="dp_sp_0">
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+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+				<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="640.6875"/>
+				<cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="520510.875"/>
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="9311861"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="399.995900105911"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1404.93721264194"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p NSI Full ms [400.00-1400.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="400" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="256">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p NSI Full ms [400.00-1400.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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diff -r d55a7181895c -r f01f84cbd265 test-data/MetaProSIP_1_output_1.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MetaProSIP_1_output_1.csv	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,7 @@
+Group 1	# Distinct Peptides	# Unambigous Proteins	Median Global LR	median RIA 1	median RIA 2
+	1	1	0.269627132474428	0.603333333333335	36.4733333333347
+	Protein Accession	Description	# Unique Peptides	Median Global LR	median RIA 1	median RIA 2
+	CONTIG23640_802236	 length=2326  numreads=28 strand:-1 frame:0 orf_location:136:990	1	0.269627132474428	0.603333333333335	36.4733333333347
+		Peptide Sequence	RT	Exp. m/z	Theo. m/z	Charge	Score	TIC fraction	#non-natural weights		RIA 1	INT 1	Cor. 1	RIA 2	INT 2	Cor. 2	Peak intensities	Global LR
+		YGGAVDPTVLGGVK	80.52	666.8623	666.861538013921	2	0.174659044235501	0.831887919884233	7		0.6	1432379	1.00	36.5	146376	0.87	659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 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 0 0 	0.269627132474428
+Non-Unique Peptides	Accessions	Peptide Sequence	Descriptions	Score	RT	Exp. m/z	Theo. m/z	Charge	#non-natural weights		Peak intensities	Global LR
diff -r d55a7181895c -r f01f84cbd265 test-data/MetaProSIP_1_output_2.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MetaProSIP_1_output_2.csv	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,3 @@
+Peptide Sequence	Feature	Quality Report Spectrum	Quality report scores	Sample Name	Protein Accessions	Description	Unique	#Ambiguity members	Score	RT	Exp. m/z	Theo. m/z	Charge	TIC fraction	#non-natural weights	Peak intensities	Group	Global Peptide LR	RIA 1	LR of RIA 1	INT 1	Cor. 1	RIA 2	LR of RIA 2	INT 2	Cor. 2	RIA 3	LR of RIA 3	INT 3	Cor. 3	RIA 4	LR of RIA 4	INT 4	Cor. 4	RIA 5	LR of RIA 5	INT 5	Cor. 5	RIA 6	LR of RIA 6	INT 6	Cor. 6	RIA 7	LR of RIA 7	INT 7	Cor. 7	RIA 8	LR of RIA 8	INT 8	Cor. 8	RIA 9	LR of RIA 9	INT 9	Cor. 9	RIA 10	LR of RIA 10	INT 10	Cor. 10
+YGGAVDPTVLGGVK	feature			test_mode_enabled.mzML	CONTIG23640_802236	 length=2326  numreads=28 strand:-1 frame:0 orf_location:136:990	1	1	0.174659044235501	80.52	666.8623	666.8615	2	0.831887919884232	7	659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 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 0 0 	0	0.269627132474428	0.6	1.0	1432378.6	1.0	36.5	0.0	146375.7	0.9
+
diff -r d55a7181895c -r f01f84cbd265 test-data/MzMLSplitter_output_part1.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MzMLSplitter_output_part1.mzML	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,222 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
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+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+	<cvList count="5">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
+		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
+		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
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+		</fileContent>
+		<contact>
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+			<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />
+		</contact>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
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+		</sample>
+	</sampleList>
+	<softwareList count="4">
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+		</software>
+		<software id="so_default" version="" >
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+		</software>
+		<software id="so_dp_sp_0_pm_0" version="" >
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+		</software>
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+		</software>
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+			<componentList count="3">
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+				</source>
+				<analyzer order="0">
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+				</analyzer>
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+			<softwareRef ref="so_in_0" />
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+	</instrumentConfigurationList>
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+				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="1999-12-31+23:59" />
+				<userParam name="parameter: mode" type="xsd:string" value="test_mode"/>
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0">
+		<spectrumList count="5" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="spectrum=1" index="0" defaultArrayLength="787" dataProcessingRef="dp_sp_0">
+				<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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+				</scanList>
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+				<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="25.3972" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="88">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+					</binaryDataArray>
+					<binaryDataArray encodedLength="44">
+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+						<binary>dFNiQxQQLkIcK5ZCCBdQQ2L91UOKGBVDhPZcQ0KtHUM=</binary>
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
+<indexList count="1">
+	<index name="spectrum">
+		<offset idRef="spectrum=1">4899</offset>
+		<offset idRef="spectrum=2">19011</offset>
+		<offset idRef="spectrum=3">31431</offset>
+		<offset idRef="spectrum=4">32961</offset>
+		<offset idRef="spectrum=5">34527</offset>
+	</index>
+</indexList>
+<indexListOffset>36171</indexListOffset>
+<fileChecksum>0</fileChecksum>
+</indexedmzML>
\ No newline at end of file
diff -r d55a7181895c -r f01f84cbd265 test-data/MzMLSplitter_output_part2.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MzMLSplitter_output_part2.mzML	Tue Mar 20 14:39:44 2018 -0400
@@ -0,0 +1,222 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+	<cvList count="5">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
+		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
+		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+		</fileContent>
+		<contact>
+			<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />
+			<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />
+		</contact>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
+			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
+		</sample>
+	</sampleList>
+	<softwareList count="4">
+		<software id="so_in_0" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_default" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_dp_sp_0_pm_0" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_dp_sp_0_pm_1" version="version_string" >
+			<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />
+		</software>
+	</softwareList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="ic_0">
+			<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+			<componentList count="3">
+				<source order="0">
+					<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />
+				</source>
+				<analyzer order="0">
+					<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />
+				</analyzer>
+				<detector order="0">
+					<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />
+				</detector>
+			</componentList>
+			<softwareRef ref="so_in_0" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="dp_sp_0">
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
+				<cvParam cvRef="MS" accession="MS:1000543" name="data processing action" />
+			</processingMethod>
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
+				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="1999-12-31+23:59" />
+				<userParam name="parameter: mode" type="xsd:string" value="test_mode"/>
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0">
+		<spectrumList count="5" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="spectrum=6" index="0" defaultArrayLength="885" dataProcessingRef="dp_sp_0">
+				<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="31.2627" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="9440">
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+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
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