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Changeset 1:8bac3cc5c5de (2019-07-20)

Previous changeset 0:d4b6c9eae635 (2013-05-10) Next changeset 2:666f3453a99d (2019-08-07)

Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847

modified:
README.md
maxquant.xml

removed:
LICENSE
README_GALAXYP.md
README_REPO.md
augment_maxquant_mods.py
build_mods_loc.py
build_proteases_loc.py
extended_modifications.xml
maxquant_mods.loc
maxquant_mods.loc.sample
maxquant_mods.loc.sample.default
maxquant_mods.loc.sample.extended
maxquant_proteases.loc
maxquant_proteases.loc.sample
maxquant_wrapper.py
modifications.xml
proteases.xml
unimod.xml
update.sh

diff -r d4b6c9eae635 -r 8bac3cc5c5de LICENSE
--- a/LICENSE Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,11 +0,0 @@
---2012-09-19 08:46:18-- http://www.apache.org/licenses/LICENSE-2.0.txt
-Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229
-Connecting to www.apache.org|140.211.11.131|:80... connected.
-HTTP request sent, awaiting response... 200 OK
-Length: 11358 (11K) [text/plain]
-Saving to: “LICENSE-2.0.txt”
-
- 0K .......... . 100% 200K=0.06s
-
-2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358]
-

diff -r d4b6c9eae635 -r 8bac3cc5c5de README.md
--- a/README.md Fri May 10 17:22:51 2013 -0400
+++ b/README.md Sat Jul 20 05:01:05 2019 -0400

@@ -1,34 +1,27 @@
-Tool wrapper for MaxQuant.
+GalaxyP - MaxQuant
+==================

-MaxQuant is a Windows only program and so you will likely need to
-deploy this tool to run on a remote Windows system via the LWR
-(https://lwr.readthedocs.org).
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
+* Tool ID: `maxquant`
+* Tool Type: `default`

-The sample mods file maxquant_mods.loc.sample corresponds to the
-default modifications MaxQuant is configured with. The Galaxy-P
-project uses a MaxQuant that has been extended with all of Unimod. To
-modify MaxQuant in this fashion replace MaxQuant's modifications.xml
-file with the extended_modifications.xml distributed with this tool
-and configure Galaxy with the maxquant_mods.loc.sample.extended loc
-file.# Obtaining Tools

-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
+Description
+-----------
+
+Wrapper for the MaxQuant version available in conda.
+

-# Contact
-
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
-
-# License
+Updating
+--------

-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
-
-# Tool Versioning
+MaxQuant often changes the layout of its parameters file.
+So changes to the code are likely to be necessary when
+updating to a new version of MaxQuant. The init.py script
+can be used to initialize the tool with a new list of
+modifications or enzymes. From the tool dir run:

-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.
+./init.py -m MODIFICATIONS.XML -e ENZYMES.XML
+
+The location of these xml files usually is:
+ANACONDA_DIR/bin/conf/
\ No newline at end of file

diff -r d4b6c9eae635 -r 8bac3cc5c5de README_GALAXYP.md
--- a/README_GALAXYP.md Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-# Obtaining Tools
-
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
-
-# Contact
-
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
-
-# License
-
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
-
-# Tool Versioning
-
-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.

diff -r d4b6c9eae635 -r 8bac3cc5c5de README_REPO.md
--- a/README_REPO.md Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-Tool wrapper for MaxQuant.
-
-MaxQuant is a Windows only program and so you will likely need to
-deploy this tool to run on a remote Windows system via the LWR
-(https://lwr.readthedocs.org).
-
-The sample mods file maxquant_mods.loc.sample corresponds to the
-default modifications MaxQuant is configured with. The Galaxy-P
-project uses a MaxQuant that has been extended with all of Unimod. To
-modify MaxQuant in this fashion replace MaxQuant's modifications.xml
-file with the extended_modifications.xml distributed with this tool
-and configure Galaxy with the maxquant_mods.loc.sample.extended loc
-file.
\ No newline at end of file

diff -r d4b6c9eae635 -r 8bac3cc5c5de augment_maxquant_mods.py
--- a/augment_maxquant_mods.py Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,166 +0,0 @@
-#!/usr/bin/env python
-"""
-Usage:
-    python augment_maxquant_mods.py
-
-Assuming Unimod XML file (unimod.xml) and stock MaxQuant modifications
-file (modifications.xml) are in this same directory, this script will
-create a new MaxQuant modifications file (extended_modifications.xml)
-with an a new modification for each unimod entry. These new entires
-will be suffixed with [Unimod] to distinguish them from existing
-MaxQuant entries. This file should be copied to
-<MaxQuant Path>\bin\conf\modifications.xml
-
-"""
-import xml.etree.ElementTree as ET
-import re
-
-FAKE_DATE = "2012-06-11T21:21:24.4946343+02:00"
-
-POSITION_MAP = {
-    "Anywhere": "anywhere",
-    "Any N-term": "anyNterm",
-    "Any C-term": "anyCterm",
-    "Protein N-term": "proteinNterm",
-    "Protein C-term": "proteinCterm",
-}
-
-unimod_tree = ET.parse('unimod.xml')
-unimod_ns = '{http://www.unimod.org/xmlns/schema/unimod_2}'
-unimod_modifications_el = unimod_tree.getroot().find('%smodifications' % unimod_ns)
-mq_tree = ET.parse("modifications.xml")
-mq_root = mq_tree.getroot()
-
-
-def to_label(title, site):
-    return "%s (%s) [Unimod]" % (title, site)
-
-
-def copy_modification(unimod_modification):
-    if unimod_modification.hidden:
-        return False
-    if unimod_modification.delta_el is None:
-        return False
-    comp_array = unimod_modification.composition_array
-    for aa, count in comp_array:
-        if len(aa) > 1 and aa not in COMP_REPLACES.keys():
-            # Complex stuff like Hep, that I cannot translate into MaxQuant.
-            return False
-    return True
-
-
-COMP_REPLACES = {
-    "15N": "Nx",
-    "13C": "Cx",
-    "18O": "Ox",
-    "2H": "Hx",
-}
-
-## HEP?
-
-
-def convert_composition(unimod_composition):
-    """
-    Convert Unimod representation of composition to MaxQuant
-    """
-    composition = unimod_composition
-    for key, value in COMP_REPLACES.iteritems():
-        composition = composition.replace(key, value)
-    print composition
-    return composition
-
-
-def populate_modification(modification, unimod_modification):
-    """
-    Copy unimod entry ``unimod_modification`` to MaxQuant entry ``modification``.
-    """
-    attrib = modification.attrib
-    attrib["create_date"] = FAKE_DATE
-    attrib["last_modified_date"] = FAKE_DATE
-    attrib["reporterCorrectionM1"] = str(0)
-    attrib["reporterCorrectionM2"] = str(0)
-    attrib["reporterCorrectionP1"] = str(0)
-    attrib["reporterCorrectionP2"] = str(0)
-    attrib["user"] = "build_mods_script"
-    label = unimod_modification.label
-    attrib["title"] = label
-    attrib["description"] = label
-    attrib["composition"] = convert_composition(unimod_modification.raw_composition)
-    unimod_position = unimod_modification.position
-    maxquant_position = POSITION_MAP[unimod_position]
-    assert maxquant_position != None
-    position_el = ET.SubElement(modification, "position")
-    position_el.text = maxquant_position
-    modification_site_el = ET.SubElement(modification, "modification_site")
-    modification_site_el.attrib["index"] = "0"
-    unimod_site = unimod_modification.site
-    modification_site_el.attrib["site"] = "-" if len(unimod_site) > 1 else unimod_site
-    type_el = ET.SubElement(modification, "type")
-    type_el.text = "standard"
-    return modification
-
-
-class UnimodModification:
-
-    def __init__(self, modification, specificity):
-        self.modification = modification
-        self.specificity = specificity
-
-    @property
-    def title(self):
-        return self.modification.attrib["title"]
-
-    @property
-    def site(self):
-        return self.specificity.attrib["site"]
-
-    @property
-    def label(self):
-        return "%s (%s) [Unimod]" % (self.title, self.site)
-
-    @property
-    def delta_el(self):
-        return self.modification.find("%sdelta" % unimod_ns)
-
-    @property
-    def raw_composition(self):
-        return self.delta_el.attrib["composition"]
-
-    @property
-    def composition_array(self):
-        raw_composition = self.raw_composition
-        aa_and_counts = re.split("\s+", raw_composition)
-        comp_array = []
-        for aa_and_count in aa_and_counts:
-            match = re.match(r"(\w+)($(-?\d+)$)?", aa_and_count)
-            aa = match.group(1)
-            count = match.group(3) or 1
-            comp_array.append((aa, count))
-        return comp_array
-
-    @property
-    def position(self):
-        return self.specificity.attrib["position"]
-
-    @property
-    def hidden(self):
-        return self.specificity.attrib["hidden"] == "true"
-
-unimod_modifications = []
-for mod in unimod_modifications_el.findall('%smod' % unimod_ns):
-    for specificity in mod.findall('%sspecificity' % unimod_ns):
-        unimod_modifications.append(UnimodModification(mod, specificity))
-
-max_index = 0
-for modification in mq_root.getchildren():
-    index = int(modification.attrib["index"])
-    max_index = max(max_index, index)
-
-for unimod_modification in unimod_modifications:
-    if copy_modification(unimod_modification):
-        print unimod_modification.composition_array
-        max_index += 1
-        modification = ET.SubElement(mq_root, "modification", attrib={"index": str(max_index)})
-        populate_modification(modification, unimod_modification)
-
-mq_tree.write("extended_modifications.xml")

diff -r d4b6c9eae635 -r 8bac3cc5c5de build_mods_loc.py
--- a/build_mods_loc.py Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,17 +0,0 @@
-#!/usr/bin/env python
-
-import xml.etree.ElementTree as ET
-from os.path import exists
-
-mods_path = "extended_modifications.xml"
-
-if not exists(mods_path):
-    mods_path = "modifications.xml"
-
-tree = ET.parse(mods_path)
-modifications_el = tree.getroot()
-
-with open("maxquant_mods.loc", "w") as output:
-    for mod in modifications_el.getchildren():
-        if mod.find("type").text.strip() == "standard":
-            output.write("%s\n" % mod.attrib["title"])

diff -r d4b6c9eae635 -r 8bac3cc5c5de build_proteases_loc.py
--- a/build_proteases_loc.py Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,14 +0,0 @@
-#!/usr/bin/env python
-
-import xml.etree.ElementTree as ET
-from os.path import exists
-
-proteases_path = "proteases.xml"
-
-tree = ET.parse(proteases_path)
-proteases_el = tree.getroot()
-
-with open("maxquant_proteases.loc", "w") as output:
- for protease in proteases_el.getchildren():
- output.write("%s\n" % protease.attrib["name"])
-

diff -r d4b6c9eae635 -r 8bac3cc5c5de extended_modifications.xml
--- a/extended_modifications.xml Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2579 +0,0 @@\n-<modifications>\n- <modification composition="C(2) H(2) O" create_date="2010-01-19T13:25:24.82357+01:00" description="Acetylation" index="0" last_modified_date="2010-01-19T14:15:40.2445414+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Acetyl (K)" user="neuhause">\n- <position>notCterm</position>\n- <modification_site index="0" site="K">\n- <diagnostic_collection>\n- <diagnostic composition="C(7) H(11) O N" name="acK*" shortname="acK*" />\n- <diagnostic composition="C(7) H(14) O N(2)" name="acK" shortname="acK" />\n- </diagnostic_collection>\n- </modification_site>\n- <type>standard</type>\n- </modification>\n- <modification composition="C(2) H(2) O" create_date="2010-01-19T14:27:34.5843488+01:00" description="Acetylation" index="1" last_modified_date="2010-01-19T14:28:09.7383488+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Acetyl (Protein N-term)" user="neuhause">\n- <position>proteinNterm</position>\n- <modification_site index="0" site="-" />\n- <type>standard</type>\n- </modification>\n- <modification composition="C(2) H(3) N O" create_date="2010-01-19T15:54:02.1976309+01:00" description="Iodoacetamide derivative" index="2" last_modified_date="2010-01-19T15:55:13.1353165+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Carbamidomethyl (C)" user="neuhause">\n- <position>anywhere</position>\n- <modification_site index="0" site="C" />\n- <type>standard</type>\n- </modification>\n- <modification composition="O " create_date="2010-01-19T14:29:05.2191728+01:00" description="Oxidation" index="3" last_modified_date="2010-01-19T20:38:21.9609829+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Oxidation (M)" user="neuhause">\n- <position>anywhere</position>\n- <modification_site index="0" site="M" />\n- <type>standard</type>\n- </modification>\n- <modification composition="H O(3) P" create_date="2010-01-19T14:34:50.0721008+01:00" description="Phosphorylation" index="4" last_modified_date="2010-01-19T20:39:28.1471599+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Phospho (STY)" user="neuhause">\n- <position>anywhere</position>\n- <modification_site index="0" site="S">\n- <neutralloss_collection>\n- <neutralloss composition="H(3) O(4) P" name="H(3) O(4) P" shortname="H3 O4 P" />\n- </neutralloss_collection>\n- </modification_site>\n- <modification_site index="1" site="T">\n- <neutralloss_collection>\n- <neutralloss composition="H(3) O(4) P" name="H(3) O(4) P" shortname="H3 O4 P" />\n- </neutralloss_collection>\n- </modification_site>\n- <modification_site index="2" site="Y">\n- <diagnostic_collection>\n- <diagnostic composition="C(8) H(10) O(4) N P" name="C(8) H(10) O(4) N P" shortname="pY" />\n- </diagnostic_collection>\n- </modification_site>\n- <type>standard</type>\n- </modification>\n- <modification composition="Cx(6) C(-6)" create_date="2010-01-19T14:37:21.2757206+01:00" description="Arginine-13C6 (R-13C6)" index="5" last_modified_date="2010-01-23T19:17:45.328125+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Arg6" user="cox">\n- <position>anywhere</position>\n- <modification_site index="0" site="R" />\n- <type>label</type>\n- </modification>\n- <modification composition="Cx(6) Nx(4) C(-6) N(-4)" create_date="2010-01-19T14:38:45.7906712+01:00" des'..b'rrectionP2="0" title="MG-H1 (R) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="R" /><type>standard</type></modification><modification composition="C(2) O" create_date="2012-06-11T21:21:24.4946343+02:00" description="G-H1 (R) [Unimod]" index="1300" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="G-H1 (R) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="R" /><type>standard</type></modification><modification composition="H(6) C(-2) Cx(6) Nx(2) O(2)" create_date="2012-06-11T21:21:24.4946343+02:00" description="Label:13C(6)15N(2)+GlyGly (K) [Unimod]" index="1301" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Label:13C(6)15N(2)+GlyGly (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(-1) Hx(4) Cx(6) N O" create_date="2012-06-11T21:21:24.4946343+02:00" description="ICPL:13C(6)2H(4) (N-term) [Unimod]" index="1302" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="ICPL:13C(6)2H(4) (N-term) [Unimod]" user="build_mods_script"><position>anyNterm</position><modification_site index="0" site="-" /><type>standard</type></modification><modification composition="H(-1) Hx(4) Cx(6) N O" create_date="2012-06-11T21:21:24.4946343+02:00" description="ICPL:13C(6)2H(4) (K) [Unimod]" index="1303" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="ICPL:13C(6)2H(4) (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(-1) Hx(4) Cx(6) N O" create_date="2012-06-11T21:21:24.4946343+02:00" description="ICPL:13C(6)2H(4) (N-term) [Unimod]" index="1304" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="ICPL:13C(6)2H(4) (N-term) [Unimod]" user="build_mods_script"><position>proteinNterm</position><modification_site index="0" site="-" /><type>standard</type></modification><modification composition="H(39) C(23) N(9) O(11)" create_date="2012-06-11T21:21:24.4946343+02:00" description="QQQTGG (K) [Unimod]" index="1305" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="QQQTGG (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(38) C(23) N(8) O(12)" create_date="2012-06-11T21:21:24.4946343+02:00" description="QEQTGG (K) [Unimod]" index="1306" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="QEQTGG (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(21) B C(20) N(4) O(3) F(2)" create_date="2012-06-11T21:21:24.4946343+02:00" description="Bodipy (C) [Unimod]" index="1307" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Bodipy (C) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="C" /><type>standard</type></modification></modifications>\n\\ No newline at end of file\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de init.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/init.py Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+"""Initialize MaxQuant tool for use with a new version of
+modifications/enzymes.xml.
+
+TODO: Append function: only add modifications that are not
+already present, add modification entries to conda maxquant
+
+Authors: Damian Glaetzer <d.glaetzer@mailbox.org>
+
+Usage: init.py [-a] [-m MODS_FILE] [-e ENZYMES_FILE]
+FILES are the modifications/enzymes.xml of MaxQuant, located at
+<ANACONDA_DIR>/pkgs/maxquant-<VERSION>/bin/conf/.
+(for conda installations)
+
+Updates modification parameters in macros.xml.
+"""
+
+import argparse
+import re
+import xml.etree.ElementTree as ET
+from xml.dom import minidom
+
+
+def build_list(node, name, mod_list, append=False):
+    """Build the modifications list in macros.xml"""
+    node.clear()
+    node.tag = 'xml'
+    node.set('name', name)
+    for m in mod_list:
+        ET.SubElement(node, 'expand', attrib={'macro': 'mod_option',
+                                              'value': m})
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-m", "--modifications",
+                    help="modifications.xml of maxquant")
+parser.add_argument("-e", "--enzymes",
+                    help="enzymes.xml of maxquant")
+args = parser.parse_args()
+
+if args.modifications:
+    mods_root = ET.parse(args.modifications).getroot()
+
+    mods = mods_root.findall('modification')
+    standard_mods = []
+    label_mods = []
+    for m in mods:
+        if (m.findtext('type') == 'Standard'
+            or m.findtext('type') == 'AaSubstitution'):
+            standard_mods.append(m.get('title'))
+        elif m.findtext('type') == 'Label':
+            label_mods.append(m.get('title'))
+
+if args.enzymes:
+    enzymes_root = ET.parse(args.enzymes).getroot()
+
+    enzymes = enzymes_root.findall('enzyme')
+    enzymes_list = [e.get('title') for e in enzymes]
+
+macros_root = ET.parse('./macros.xml').getroot()
+for child in macros_root:
+    if child.get('name') == 'modification' and args.modifications:
+        build_list(child, 'modification', standard_mods)
+    elif child.get('name') == 'label' and args.modifications:
+        build_list(child, 'label', label_mods)
+    elif child.get('name') == 'proteases' and args.enzymes:
+        build_list(child, 'proteases', enzymes_list)
+
+rough_string = ET.tostring(macros_root, 'utf-8')
+reparsed = minidom.parseString(rough_string)
+pretty = reparsed.toprettyxml(indent="    ")
+even_prettier = re.sub(r"\n\s+\n", r"\n", pretty)
+with open('./macros.xml', 'w') as f:
+    print(even_prettier, file=f)

diff -r d4b6c9eae635 -r 8bac3cc5c5de macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Jul 20 05:01:05 2019 -0400

[

b'@@ -0,0 +1,485 @@\n+<?xml version="1.0" ?>\n+<macros>\n+ <token name="@VERSION@">1.6.3.4</token>\n+ <token name="@SUBSTITUTION_RX@">[^\\w\\-\\s\\.]</token>\n+ <xml name="output" token_format="tabular" token_label="default description" token_name="default">\n+ <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n+ <filter>\'@NAME@\' in output_opts[\'output\']</filter>\n+ </data>\n+ </xml>\n+ <xml name="output_option" token_label="default label" token_name="default">\n+ <option value="@NAME@">@LABEL@</option>\n+ </xml>\n+ <xml name="mod_option" token_value="default">\n+ <option value="@VALUE@">@VALUE@</option>\n+ </xml>\n+ <xml name="modification">\n+ <expand macro="mod_option" value="Acetyl (K)"/>\n+ <expand macro="mod_option" value="Acetyl (Protein N-term)"/>\n+ <expand macro="mod_option" value="Carbamidomethyl (C)"/>\n+ <expand macro="mod_option" value="Oxidation (M)"/>\n+ <expand macro="mod_option" value="Phospho (STY)"/>\n+ <expand macro="mod_option" value="GlyGly (K)"/>\n+ <expand macro="mod_option" value="Methyl (KR)"/>\n+ <expand macro="mod_option" value="Dimethyl (KR)"/>\n+ <expand macro="mod_option" value="Trimethyl (K)"/>\n+ <expand macro="mod_option" value="Pro5"/>\n+ <expand macro="mod_option" value="Pro6"/>\n+ <expand macro="mod_option" value="Glu->pyro-Glu"/>\n+ <expand macro="mod_option" value="Gln->pyro-Glu"/>\n+ <expand macro="mod_option" value="QQTGG (K)"/>\n+ <expand macro="mod_option" value="Deamidation (N)"/>\n+ <expand macro="mod_option" value="Deamidation 18O (N)"/>\n+ <expand macro="mod_option" value="Deamidation (NQ)"/>\n+ <expand macro="mod_option" value="Hydroxyproline"/>\n+ <expand macro="mod_option" value="Carbamyl (N-term)"/>\n+ <expand macro="mod_option" value="Delta:H(2)C(2) (N-term)"/>\n+ <expand macro="mod_option" value="Dioxidation (MW)"/>\n+ <expand macro="mod_option" value="Trioxidation (C)"/>\n+ <expand macro="mod_option" value="Dethiomethyl (M)"/>\n+ <expand macro="mod_option" value="Cation:Na (DE)"/>\n+ <expand macro="mod_option" value="Methyl (E)"/>\n+ <expand macro="mod_option" value="Dehydrated (ST)"/>\n+ <expand macro="mod_option" value="Oxidation (P)"/>\n+ <expand macro="mod_option" value="Dimethyl (K)"/>\n+ <expand macro="mod_option" value="Amidated (Protein C-term)"/>\n+ <expand macro="mod_option" value="Sulfo (STY)"/>\n+ <expand macro="mod_option" value="Acetyl (N-term)"/>\n+ <expand macro="mod_option" value="Amidated (C-term)"/>\n+ <expand macro="mod_option" value="Sulfation (Y)"/>\n+ <expand macro="mod_option" value="Phospho (ST)"/>\n+ <expand macro="mod_option" value="Cys-Cys"/>\n+ <expand macro="mod_option" value="Ala->Arg"/>\n+ <expand macro="mod_option" value="Ala->Asn"/>\n+ <expand macro="mod_option" value="Ala->Asp"/>\n+ <expand macro="mod_option" value="Ala->Cys"/>\n+ <expand macro="mod_option" value="Ala->Gln"/>\n+ <expand macro="mod_option" value="Ala->Glu"/>\n+ <expand macro="mod_option" value="Ala->Gly"/>\n+ <expand macro="mod_option" value="Ala->His"/>\n+ <expand macro="mod_option" value="Ala->Xle"/>\n+ <expand macro="mod_option" value="Ala->Lys"/>\n+ <expand macro="mod_option" value="Ala->Met"/>\n+ <expand macro="mod_option" value="Ala->Phe"/>\n+ <expand macro="mod_option" value="Ala->Pro"/>\n+ <expand macro="mod_option" value="Ala->Ser"/>\n+ <expand macro="mod_option" value="Ala->Thr"/>\n+ <expand macro="mod_option" value="Ala->Trp"/>\n+ <expand macro="mod_option" value="Ala->Tyr"/>\n+ <expand macro="mod_option" value="Ala->Val"/>\n+ <expand macro="mod_option" value="Arg->Ala"/>\n+ <expand macro="mod_option" value="Ar'..b'ption" value="CamCys->Val"/>\n+ <expand macro="mod_option" value="CamCys->Xle"/>\n+ <expand macro="mod_option" value="Ala->CamCys"/>\n+ <expand macro="mod_option" value="Arg->CamCys"/>\n+ <expand macro="mod_option" value="Asn->CamCys"/>\n+ <expand macro="mod_option" value="Asp->CamCys"/>\n+ <expand macro="mod_option" value="Gln->CamCys"/>\n+ <expand macro="mod_option" value="Glu->CamCys"/>\n+ <expand macro="mod_option" value="Gly->CamCys"/>\n+ <expand macro="mod_option" value="His->CamCys"/>\n+ <expand macro="mod_option" value="Lys->CamCys"/>\n+ <expand macro="mod_option" value="Met->CamCys"/>\n+ <expand macro="mod_option" value="Phe->CamCys"/>\n+ <expand macro="mod_option" value="Pro->CamCys"/>\n+ <expand macro="mod_option" value="Ser->CamCys"/>\n+ <expand macro="mod_option" value="Thr->CamCys"/>\n+ <expand macro="mod_option" value="Trp->CamCys"/>\n+ <expand macro="mod_option" value="Tyr->CamCys"/>\n+ <expand macro="mod_option" value="Val->CamCys"/>\n+ <expand macro="mod_option" value="Xle->CamCys"/>\n+ <expand macro="mod_option" value="Cysteinyl"/>\n+ <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>\n+ </xml>\n+ <xml name="label">\n+ <expand macro="mod_option" value="Arg6"/>\n+ <expand macro="mod_option" value="Arg10"/>\n+ <expand macro="mod_option" value="Lys4"/>\n+ <expand macro="mod_option" value="Lys6"/>\n+ <expand macro="mod_option" value="Lys8"/>\n+ <expand macro="mod_option" value="DimethLys0"/>\n+ <expand macro="mod_option" value="DimethNter0"/>\n+ <expand macro="mod_option" value="DimethLys4"/>\n+ <expand macro="mod_option" value="DimethNter4"/>\n+ <expand macro="mod_option" value="DimethLys8"/>\n+ <expand macro="mod_option" value="DimethNter8"/>\n+ <expand macro="mod_option" value="18O"/>\n+ <expand macro="mod_option" value="ICAT-0"/>\n+ <expand macro="mod_option" value="ICAT-9"/>\n+ <expand macro="mod_option" value="ICPL-Lys0"/>\n+ <expand macro="mod_option" value="ICPL-Nter0"/>\n+ <expand macro="mod_option" value="ICPL-Lys4"/>\n+ <expand macro="mod_option" value="ICPL-Nter4"/>\n+ <expand macro="mod_option" value="ICPL-Lys6"/>\n+ <expand macro="mod_option" value="ICPL-Nter6"/>\n+ <expand macro="mod_option" value="ICPL-Lys10"/>\n+ <expand macro="mod_option" value="ICPL-Nter10"/>\n+ <expand macro="mod_option" value="mTRAQ-Lys0"/>\n+ <expand macro="mod_option" value="mTRAQ-Nter0"/>\n+ <expand macro="mod_option" value="mTRAQ-Lys4"/>\n+ <expand macro="mod_option" value="mTRAQ-Nter4"/>\n+ <expand macro="mod_option" value="mTRAQ-Lys8"/>\n+ <expand macro="mod_option" value="mTRAQ-Nter8"/>\n+ <expand macro="mod_option" value="DimethLys2"/>\n+ <expand macro="mod_option" value="DimethNter2"/>\n+ <expand macro="mod_option" value="DimethLys6"/>\n+ <expand macro="mod_option" value="DimethNter6"/>\n+ <expand macro="mod_option" value="Leu7"/>\n+ <expand macro="mod_option" value="Ile7"/>\n+ </xml>\n+ <xml name="proteases">\n+ <expand macro="mod_option" value="Trypsin"/>\n+ <expand macro="mod_option" value="Trypsin/P"/>\n+ <expand macro="mod_option" value="LysC"/>\n+ <expand macro="mod_option" value="LysC/P"/>\n+ <expand macro="mod_option" value="D.P"/>\n+ <expand macro="mod_option" value="ArgC"/>\n+ <expand macro="mod_option" value="AspC"/>\n+ <expand macro="mod_option" value="GluC"/>\n+ <expand macro="mod_option" value="GluN"/>\n+ <expand macro="mod_option" value="AspN"/>\n+ <expand macro="mod_option" value="LysN"/>\n+ <expand macro="mod_option" value="Chymotrypsin+"/>\n+ <expand macro="mod_option" value="Chymotrypsin"/>\n+ </xml>\n+</macros>\n+\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant.xml
--- a/maxquant.xml Fri May 10 17:22:51 2013 -0400
+++ b/maxquant.xml Sat Jul 20 05:01:05 2019 -0400

[

b'@@ -1,331 +1,364 @@\n-<tool id="maxquant" version="0.1.0" name="MaxQuant">\n- <description>\n- </description>\n- <requirements>\n- <requirement>maxquant</requirement>\n- <requirement type="platform">windows</requirement>\n- </requirements>\n- <configfiles>\n- <configfile name="inputs_config">##Describe inputs\n-#set $type = str($analysis_type.type)\n-#if $type == "single"\n-#set $groups = [$analysis_type]\n-#elif $type == "multi_same"\n-#set $groups = $analysis_type.groups\n-#end if\n-#for $i, $group in enumerate($groups)\n-num:${str(i + 1)}\n-#for $input in $group.inputs\n-name:${input.display_name}\n-path:${input}\n-#end for\n-#end for\n-</configfile>\n- </configfiles>\n- <command interpreter="python">maxquant_wrapper.py \n- --input_groups=$inputs_config\n- --database="${database}"\n- --database_name="${database.name}"\n- --protease=$analysis_type.protease\n- --first_search_tol=$analysis_type.first_search_tol\n- --main_search_tol=$analysis_type.main_search_tol\n- --max_missed_cleavages=$analysis_type.max_missed_cleavages\n- --max_n_mods=$analysis_type.max_n_mods\n- --variable_mods="${analysis_type.variable_modifications or \'\'}"\n- #if $analysis_type.advanced_group_parameters.specify\n- --do_mass_filtering=$analysis_type.advanced_group_parameters.do_mass_filtering\n- --max_charge=$analysis_type.advanced_group_parameters.max_charge\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@">\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">maxquant</requirement>\n+ <requirement type="package" version="3.7">python</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #import re\n+\n+ python3 \'$__tool_directory__/mqwrapper.py\'\n+ --num_threads=\\${GALAXY_SLOTS:-1}\n+ --substitution_rx=\'@SUBSTITUTION_RX@\'\n+ #if $input_opts.infile.select == "mzxml_files"\n+ --mzxml_files=\'$input_opts.infile.mzxml_files\'\n+ #set names = \',\'.join([re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($name.element_identifier)) for $name in $input_opts.infile.mzxml_files])\n+ #else\n+ --raw_files=\'$input_opts.infile.raw_files\'\n+ #set names = \',\'.join([re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($name.element_identifier)) for $name in $input_opts.infile.raw_files])\n+ #end if\n+ --infile_names=\'$names\'\n+ --version=\'@VERSION@\'\n+ --fasta_files=\'$input_opts.fasta_files\'\n+ --identifier_parse_rule=\'$input_opts.identifier_parse_rule\'\n+ --description_parse_rule=\'$input_opts.description_parse_rule\'\n+\n+ --exp_design=\'$search_opts.template\'\n+ --missed_cleavages=$search_opts.missed_cleavages\n+ --min_peptide_len=$search_opts.min_peptide_len\n+ --max_peptide_mass=$search_opts.max_peptide_mass\n+ --min_unique_pep=$search_opts.min_unique_pep\n+ $search_opts.calc_peak_properties\n+ $search_opts.match_between_runs\n+ #if $search_opts.fixed_mods\n+ --fixed_mods=\'$search_opts.fixed_mods\'\n+ #end if\n+ #if $search_opts.var_mods\n+ --var_mods=\'$search_opts.var_mods\'\n+ #end if\n+ #if $search_opts.proteases\n+ --proteases=\'$search_opts.proteases\'\n+ #end if\n+ #if $search_opts.silac.light_mods\n+ --light_mods=\'$search_opts.silac.light_mods\'\n #end if\n- #set $run = $analysis_type.run\n- #set $lcms_run_type = $run.lcms_run_type\n- --lcms_run_type=$lcms_run_type\n- #if str($lcms_run_type) != "3"\n- ## i.e. is not reporter ion type\n- #if $run.labels_conditional.labeled\n- #for $label_group in $run.labels_conditional.label_groups\n- --labels="${label_group.labels or \'\'}"\n- #end for\n- --max_labeled_aa=$run.labels_conditional.max_labeled_aa\n+ #if $search_opts.silac.medium_mods\n+ --medium_mods=\'$search_opts.silac.medium_mods\'\n+ #end if\n+ #if $search_opts.silac.heavy_mods\n+ --heavy_mods=\'$search_opts.silac.heavy_mods\'\n #end if\n- #else\n- --reporter_type=$run.reporter_type\n- #end if \n- #set $sp'..b' <param name="proteases" value="Trypsin/P" />\n+ <param name="write_mztab" value="true" />\n+ <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />\n+ <output name="evidence" file="single/combined/txt/evidence.txt" />\n+ <output name="msms" file="single/combined/txt/msms.txt" />\n+ <output name="mzTab" file="single/combined/txt/mzTab.mzTab" lines_diff="4"/>\n+ <output name="allPeptides" file="single/combined/txt/allPeptides.txt" />\n+ <output name="msmsScans" file="single/combined/txt/msmsScans.txt" />\n+ <output name="mzRange" file="single/combined/txt/mzRange.txt" />\n+ <output name="parameters" file="single/combined/txt/parameters.txt" lines_diff="10"/>\n+ <output name="peptides" file="single/combined/txt/peptides.txt" />\n+ <output name="peptideSection" file="single/combined/txt/peptideSection.txt" />\n+ <output name="proteinGroups" file="single/combined/txt/proteinGroups.txt" />\n+ <output name="summary" file="single/combined/txt/summary.txt" />\n+ <output name="modificationSpecificPeptides" file="single/combined/txt/modificationSpecificPeptides.txt" />\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. \n+\n+This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a very reduced set of search parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too. If possible, this tool should be preferred. \n+\n+**Input files**\n+\n+- Thermo raw file or mzXML file\n+ - The datatype has to be \'thermo.raw\' or \'mzXML\'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)\n+- Optional files:\n+ - Tabular file with experimental design template: \n+ - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Fraction are abitrary strings, Experiment is an integer, PTM is either True or False.\n+\n+ ::\n+\n+ Name Fraction Experiment PTM\n+ File1 1 E1 False\n+ File2 2 E1 False\n+ File3 3 E1 False\n+ ...\n+ ...\n+\n+**Parameter Options**\n+\n+- Quantification options\n+ - label based: \n+ - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections\n+ - label-free\n+\n+**Output files**\n+\n+Different output file options are available, most of them are part of the MaxQuant txt directory. \n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+ @article{cox2008maxquant,\n+ title={MaxQuant enables high peptide identification rates, individualized\n+ ppb-range mass accuracies and proteome-wide protein quantification},\n+ author={Cox, J{\\"u}rgen and Mann, Matthias},\n+ journal={Nature biotechnology},\n+ volume={26},\n+ number={12},\n+ pages={1367},\n+ year={2008},\n+ publisher={Nature Publishing Group}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @article{tyanova2016maxquant,\n+ title={The MaxQuant computational platform for mass\n+ spectrometry-based shotgun proteomics},\n+ author={Tyanova, Stefka and Temu, Tikira and Cox, J{\\"u}rgen},\n+ journal={Nature protocols},\n+ volume={11},\n+ number={12},\n+ pages={2301},\n+ year={2016},\n+ publisher={Nature Publishing Group}\n+ }\n+ </citation>\n+ </citations>\n </tool>\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_mods.loc
--- a/maxquant_mods.loc Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1234 +0,0 @@\n-Acetyl (K)\n-Acetyl (Protein N-term)\n-Carbamidomethyl (C)\n-Oxidation (M)\n-Phospho (STY)\n-GlyGly (K)\n-Methyl (KR)\n-Dimethyl (KR)\n-Trimethyl (K)\n-Pro5\n-Pro6\n-Glu->pyro-Glu\n-Gln->pyro-Glu\n-OHexNAc\n-QQTGG (K)\n-Deamidation (N)\n-Deamidation 18O (N)\n-Deamidation (NQ)\n-Ala->Arg\n-Ala->Asn\n-Ala->Asp\n-Ala->Cys\n-Ala->Gln\n-Ala->Glu\n-Ala->Gly\n-Ala->His\n-Ala->Xle\n-Ala->Lys\n-Ala->Met\n-Ala->Phe\n-Ala->Pro\n-Ala->Ser\n-Ala->Thr\n-Ala->Trp\n-Ala->Tyr\n-Ala->Val\n-Arg->Ala\n-Arg->Asn\n-Arg->Asp\n-Arg->Cys\n-Arg->Gln\n-Arg->Glu\n-Arg->Gly\n-Arg->His\n-Arg->Lys\n-Arg->Met\n-Arg->Phe\n-Arg->Pro\n-Arg->Ser\n-Arg->Thr\n-Arg->Trp\n-Arg->Tyr\n-Arg->Val\n-Arg->Xle\n-Asn->Ala\n-Asn->Arg\n-Asn->Asp\n-Asn->Cys\n-Asn->Gln\n-Asn->Glu\n-Asn->Gly\n-Asn->His\n-Asn->Lys\n-Asn->Met\n-Asn->Phe\n-Asn->Pro\n-Asn->Ser\n-Asn->Thr\n-Asn->Trp\n-Asn->Tyr\n-Asn->Val\n-Asn->Xle\n-Asp->Ala\n-Asp->Arg\n-Asp->Asn\n-Asp->Cys\n-Asp->Gln\n-Asp->Glu\n-Asp->Gly\n-Asp->His\n-Asp->Lys\n-Asp->Met\n-Asp->Phe\n-Asp->Pro\n-Asp->Ser\n-Asp->Thr\n-Asp->Trp\n-Asp->Tyr\n-Asp->Val\n-Asp->Xle\n-Cys->Ala\n-Cys->Arg\n-Cys->Asn\n-Cys->Asp\n-Cys->Gln\n-Cys->Glu\n-Cys->Gly\n-Cys->His\n-Cys->Lys\n-Cys->Met\n-Cys->Phe\n-Cys->Pro\n-Cys->Ser\n-Cys->Thr\n-Cys->Trp\n-Cys->Tyr\n-Cys->Val\n-Cys->Xle\n-Gln->Ala\n-Gln->Arg\n-Gln->Asn\n-Gln->Asp\n-Gln->Cys\n-Gln->Glu\n-Gln->Gly\n-Gln->His\n-Gln->Lys\n-Gln->Met\n-Gln->Phe\n-Gln->Pro\n-Gln->Ser\n-Gln->Thr\n-Gln->Trp\n-Gln->Tyr\n-Gln->Val\n-Gln->Xle\n-Glu->Ala\n-Glu->Arg\n-Glu->Asn\n-Glu->Asp\n-Glu->Cys\n-Glu->Gln\n-Glu->Gly\n-Glu->His\n-Glu->Lys\n-Glu->Met\n-Glu->Phe\n-Glu->Pro\n-Glu->Ser\n-Glu->Thr\n-Glu->Trp\n-Glu->Tyr\n-Glu->Val\n-Glu->Xle\n-Gly->Ala\n-Gly->Arg\n-Gly->Asn\n-Gly->Asp\n-Gly->Cys\n-Gly->Gln\n-Gly->Glu\n-Gly->His\n-Gly->Lys\n-Gly->Met\n-Gly->Phe\n-Gly->Pro\n-Gly->Ser\n-Gly->Thr\n-Gly->Trp\n-Gly->Tyr\n-Gly->Val\n-Gly->Xle\n-His->Ala\n-His->Arg\n-His->Asn\n-His->Asp\n-His->Cys\n-His->Gln\n-His->Glu\n-His->Gly\n-His->Lys\n-His->Met\n-His->Phe\n-His->Pro\n-His->Ser\n-His->Thr\n-His->Trp\n-His->Tyr\n-His->Val\n-His->Xle\n-Lys->Ala\n-Lys->Arg\n-Lys->Asn\n-Lys->Asp\n-Lys->Cys\n-Lys->Gln\n-Lys->Glu\n-Lys->Gly\n-Lys->His\n-Lys->Met\n-Lys->Phe\n-Lys->Pro\n-Lys->Ser\n-Lys->Thr\n-Lys->Trp\n-Lys->Tyr\n-Lys->Val\n-Lys->Xle\n-Met->Ala\n-Met->Arg\n-Met->Asn\n-Met->Asp\n-Met->Cys\n-Met->Gln\n-Met->Glu\n-Met->Gly\n-Met->His\n-Met->Lys\n-Met->Phe\n-Met->Pro\n-Met->Ser\n-Met->Thr\n-Met->Trp\n-Met->Tyr\n-Met->Val\n-Met->Xle\n-Phe->Ala\n-Phe->Arg\n-Phe->Asn\n-Phe->Asp\n-Phe->Cys\n-Phe->Gln\n-Phe->Glu\n-Phe->Gly\n-Phe->His\n-Phe->Lys\n-Phe->Met\n-Phe->Pro\n-Phe->Ser\n-Phe->Thr\n-Phe->Trp\n-Phe->Tyr\n-Phe->Val\n-Phe->Xle\n-Pro->Ala\n-Pro->Arg\n-Pro->Asn\n-Pro->Asp\n-Pro->Cys\n-Pro->Gln\n-Pro->Glu\n-Pro->Gly\n-Pro->His\n-Pro->Lys\n-Pro->Met\n-Pro->Phe\n-Pro->Ser\n-Pro->Thr\n-Pro->Trp\n-Pro->Tyr\n-Pro->Val\n-Pro->Xle\n-Ser->Ala\n-Ser->Arg\n-Ser->Asn\n-Ser->Asp\n-Ser->Cys\n-Ser->Gln\n-Ser->Glu\n-Ser->Gly\n-Ser->His\n-Ser->Lys\n-Ser->Met\n-Ser->Phe\n-Ser->Pro\n-Ser->Thr\n-Ser->Trp\n-Ser->Tyr\n-Ser->Val\n-Ser->Xle\n-Thr->Ala\n-Thr->Arg\n-Thr->Asn\n-Thr->Asp\n-Thr->Cys\n-Thr->Gln\n-Thr->Glu\n-Thr->Gly\n-Thr->His\n-Thr->Lys\n-Thr->Met\n-Thr->Phe\n-Thr->Pro\n-Thr->Ser\n-Thr->Trp\n-Thr->Tyr\n-Thr->Val\n-Thr->Xle\n-Trp->Ala\n-Trp->Arg\n-Trp->Asn\n-Trp->Asp\n-Trp->Cys\n-Trp->Gln\n-Trp->Glu\n-Trp->Gly\n-Trp->His\n-Trp->Lys\n-Trp->Met\n-Trp->Phe\n-Trp->Pro\n-Trp->Ser\n-Trp->Thr\n-Trp->Tyr\n-Trp->Val\n-Trp->Xle\n-Tyr->Ala\n-Tyr->Arg\n-Tyr->Asn\n-Tyr->Asp\n-Tyr->Cys\n-Tyr->Gln\n-Tyr->Glu\n-Tyr->Gly\n-Tyr->His\n-Tyr->Lys\n-Tyr->Met\n-Tyr->Phe\n-Tyr->Pro\n-Tyr->Ser\n-Tyr->Thr\n-Tyr->Trp\n-Tyr->Val\n-Tyr->Xle\n-Val->Ala\n-Val->Arg\n-Val->Asn\n-Val->Asp\n-Val->Cys\n-Val->Gln\n-Val->Glu\n-Val->Gly\n-Val->His\n-Val->Lys\n-Val->Met\n-Val->Phe\n-Val->Pro\n-Val->Ser\n-Val->Thr\n-Val->Trp\n-Val->Tyr\n-Val->Xle\n-Xle->Ala\n-Xle->Arg\n-Xle->Asn\n-Xle->Asp\n-Xle->Cys\n-Xle->Gln\n-Xle->Glu\n-Xle->Gly\n-Xle->His\n-Xle->Lys\n-Xle->Met\n-Xle->Phe\n-Xle->Pro\n-Xle->Ser\n-Xle->Thr\n-Xle->Trp\n-Xle->Tyr\n-Xle->Val\n-CamCys->Ala\n-CamCys->Arg\n-CamCys->Asn\n-CamCys->Asp\n-CamCys->Gln\n-CamCys->Glu\n-CamCys->Gly\n-CamCys->His\n-CamCys->Lys\n-CamCys->Met\n-CamCys->Phe\n-CamCys->Pro\n-CamCys->Ser\n-CamCys->Thr\n-CamCys->Trp\n-CamCys->Tyr\n-CamCys->Val\n-CamCys->Xle\n-Ala->CamCys\n-Arg->CamCys\n-Asn->CamCys\n-Asp->CamCys\n-Gln->CamCys\n'..b'r->Pro (T) [Unimod]\n-Thr->Met (T) [Unimod]\n-Thr->Ile (T) [Unimod]\n-Thr->Arg (T) [Unimod]\n-Val->Phe (V) [Unimod]\n-Val->Ala (V) [Unimod]\n-Val->Glu (V) [Unimod]\n-Val->Met (V) [Unimod]\n-Val->Asp (V) [Unimod]\n-Val->Ile (V) [Unimod]\n-Val->Gly (V) [Unimod]\n-Trp->Ser (W) [Unimod]\n-Trp->Cys (W) [Unimod]\n-Trp->Arg (W) [Unimod]\n-Trp->Gly (W) [Unimod]\n-Trp->Leu (W) [Unimod]\n-Tyr->Phe (Y) [Unimod]\n-Tyr->Ser (Y) [Unimod]\n-Tyr->Asn (Y) [Unimod]\n-Tyr->His (Y) [Unimod]\n-Tyr->Asp (Y) [Unimod]\n-Tyr->Cys (Y) [Unimod]\n-NA-LNO2 (C) [Unimod]\n-NA-LNO2 (H) [Unimod]\n-NA-OA-NO2 (C) [Unimod]\n-NA-OA-NO2 (H) [Unimod]\n-ICPL:2H(4) (N-term) [Unimod]\n-ICPL:2H(4) (N-term) [Unimod]\n-ICPL:2H(4) (K) [Unimod]\n-iTRAQ8plex (Y) [Unimod]\n-iTRAQ8plex (N-term) [Unimod]\n-iTRAQ8plex (K) [Unimod]\n-Label:13C(6)15N(1) (I) [Unimod]\n-Label:13C(6)15N(1) (L) [Unimod]\n-Label:2H(9)13C(6)15N(2) (K) [Unimod]\n-HNE-Delta:H(2)O (K) [Unimod]\n-HNE-Delta:H(2)O (H) [Unimod]\n-HNE-Delta:H(2)O (C) [Unimod]\n-4-ONE (K) [Unimod]\n-4-ONE (H) [Unimod]\n-4-ONE (C) [Unimod]\n-O-Dimethylphosphate (Y) [Unimod]\n-O-Dimethylphosphate (T) [Unimod]\n-O-Dimethylphosphate (S) [Unimod]\n-O-Methylphosphate (Y) [Unimod]\n-O-Methylphosphate (T) [Unimod]\n-O-Methylphosphate (S) [Unimod]\n-O-Diethylphosphate (Y) [Unimod]\n-O-Diethylphosphate (T) [Unimod]\n-O-Diethylphosphate (S) [Unimod]\n-O-Ethylphosphate (Y) [Unimod]\n-O-Ethylphosphate (T) [Unimod]\n-O-Ethylphosphate (S) [Unimod]\n-O-pinacolylmethylphosphonate (Y) [Unimod]\n-O-pinacolylmethylphosphonate (T) [Unimod]\n-O-pinacolylmethylphosphonate (S) [Unimod]\n-Methylphosphonate (Y) [Unimod]\n-Methylphosphonate (T) [Unimod]\n-Methylphosphonate (S) [Unimod]\n-O-Isopropylmethylphosphonate (Y) [Unimod]\n-O-Isopropylmethylphosphonate (T) [Unimod]\n-O-Isopropylmethylphosphonate (S) [Unimod]\n-iTRAQ8plex:13C(6)15N(2) (Y) [Unimod]\n-iTRAQ8plex:13C(6)15N(2) (N-term) [Unimod]\n-iTRAQ8plex:13C(6)15N(2) (K) [Unimod]\n-DTT_ST (S) [Unimod]\n-DTT_ST (T) [Unimod]\n-Ethanolamine (D) [Unimod]\n-Ethanolamine (C-term) [Unimod]\n-Ethanolamine (E) [Unimod]\n-TMT6plex (K) [Unimod]\n-TMT6plex (N-term) [Unimod]\n-DTT_C (C) [Unimod]\n-TMT2plex (N-term) [Unimod]\n-TMT2plex (K) [Unimod]\n-TMT (N-term) [Unimod]\n-TMT (K) [Unimod]\n-ExacTagThiol (C) [Unimod]\n-ExacTagAmine (K) [Unimod]\n-NO_SMX_SEMD (C) [Unimod]\n-4-ONE+Delta:H(-2)O(-1) (K) [Unimod]\n-4-ONE+Delta:H(-2)O(-1) (H) [Unimod]\n-4-ONE+Delta:H(-2)O(-1) (C) [Unimod]\n-NO_SMX_SMCT (C) [Unimod]\n-NO_SMX_SIMD (C) [Unimod]\n-Malonyl (C) [Unimod]\n-Malonyl (S) [Unimod]\n-3sulfo (N-term) [Unimod]\n-trifluoro (L) [Unimod]\n-TNBS (N-term) [Unimod]\n-TNBS (K) [Unimod]\n-Biotin-phenacyl (C) [Unimod]\n-Biotin-phenacyl (H) [Unimod]\n-Biotin-phenacyl (S) [Unimod]\n-DTT_C:2H(6) (C) [Unimod]\n-lapachenole (C) [Unimod]\n-Label:13C(5) (P) [Unimod]\n-maleimide (K) [Unimod]\n-maleimide (C) [Unimod]\n-DTT_ST:2H(6) (T) [Unimod]\n-DTT_ST:2H(6) (S) [Unimod]\n-Met-loss (M) [Unimod]\n-Met-loss+Acetyl (M) [Unimod]\n-Menadione-HQ (K) [Unimod]\n-Menadione-HQ (C) [Unimod]\n-Carboxymethyl:13C(2) (C) [Unimod]\n-NEM:2H(5) (C) [Unimod]\n-Gly-loss+Amide (G) [Unimod]\n-TMPP-Ac (N-term) [Unimod]\n-Label:13C(6)+GlyGly (K) [Unimod]\n-Arg->Npo (R) [Unimod]\n-Label:2H(4)+Acetyl (K) [Unimod]\n-Pentylamine (Q) [Unimod]\n-PentylamineBiotin (Q) [Unimod]\n-Dihydroxyimidazolidine (R) [Unimod]\n-DFDNB (Q) [Unimod]\n-DFDNB (N) [Unimod]\n-DFDNB (R) [Unimod]\n-DFDNB (K) [Unimod]\n-Cy3b-maleimide (C) [Unimod]\n-AEC-MAEC:2H(4) (S) [Unimod]\n-AEC-MAEC:2H(4) (T) [Unimod]\n-BMOE (C) [Unimod]\n-Biotin-PEO4-hydrazide (C-term) [Unimod]\n-Label:13C(6)+Acetyl (K) [Unimod]\n-Label:13C(6)15N(2)+Acetyl (K) [Unimod]\n-EQIGG (K) [Unimod]\n-cGMP (C) [Unimod]\n-cGMP+RMP-loss (C) [Unimod]\n-Arg2PG (R) [Unimod]\n-Label:2H(4)+GlyGly (K) [Unimod]\n-Label:13C(8)15N(2) (R) [Unimod]\n-Label:13C(1)2H(3) (M) [Unimod]\n-ZGB (K) [Unimod]\n-ZGB (N-term) [Unimod]\n-MG-H1 (R) [Unimod]\n-G-H1 (R) [Unimod]\n-Label:13C(6)15N(2)+GlyGly (K) [Unimod]\n-ICPL:13C(6)2H(4) (N-term) [Unimod]\n-ICPL:13C(6)2H(4) (K) [Unimod]\n-ICPL:13C(6)2H(4) (N-term) [Unimod]\n-QQQTGG (K) [Unimod]\n-QEQTGG (K) [Unimod]\n-Bodipy (C) [Unimod]\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_mods.loc.sample
--- a/maxquant_mods.loc.sample Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,396 +0,0 @@
-Oxidation (M)
-Acetyl (Protein N-term)
-Acetyl (K)
-Ala->Arg
-Ala->Asn
-Ala->Asp
-Ala->CamCys
-Ala->Cys
-Ala->Gln
-Ala->Glu
-Ala->Gly
-Ala->His
-Ala->Lys
-Ala->Met
-Ala->Phe
-Ala->Pro
-Ala->Ser
-Ala->Thr
-Ala->Trp
-Ala->Tyr
-Ala->Val
-Ala->Xle
-Arg->Ala
-Arg->Asn
-Arg->Asp
-Arg->CamCys
-Arg->Cys
-Arg->Gln
-Arg->Glu
-Arg->Gly
-Arg->His
-Arg->Lys
-Arg->Met
-Arg->Phe
-Arg->Pro
-Arg->Ser
-Arg->Thr
-Arg->Trp
-Arg->Tyr
-Arg->Val
-Arg->Xle
-Asn->Ala
-Asn->Arg
-Asn->Asp
-Asn->CamCys
-Asn->Cys
-Asn->Gln
-Asn->Glu
-Asn->Gly
-Asn->His
-Asn->Lys
-Asn->Met
-Asn->Phe
-Asn->Pro
-Asn->Ser
-Asn->Thr
-Asn->Trp
-Asn->Tyr
-Asn->Val
-Asn->Xle
-Asp->Ala
-Asp->Arg
-Asp->Asn
-Asp->CamCys
-Asp->Cys
-Asp->Gln
-Asp->Glu
-Asp->Gly
-Asp->His
-Asp->Lys
-Asp->Met
-Asp->Phe
-Asp->Pro
-Asp->Ser
-Asp->Thr
-Asp->Trp
-Asp->Tyr
-Asp->Val
-Asp->Xle
-CamCys->Ala
-CamCys->Arg
-CamCys->Asn
-CamCys->Asp
-CamCys->Gln
-CamCys->Glu
-CamCys->Gly
-CamCys->His
-CamCys->Lys
-CamCys->Met
-CamCys->Phe
-CamCys->Pro
-CamCys->Ser
-CamCys->Thr
-CamCys->Trp
-CamCys->Tyr
-CamCys->Val
-CamCys->Xle
-Carbamidomethyl (C)
-Cys->Ala
-Cys->Arg
-Cys->Asn
-Cys->Asp
-Cys->Gln
-Cys->Glu
-Cys->Gly
-Cys->His
-Cys->Lys
-Cys->Met
-Cys->Phe
-Cys->Pro
-Cys->Ser
-Cys->Thr
-Cys->Trp
-Cys->Tyr
-Cys->Val
-Cys->Xle
-Deamidation (N)
-Deamidation (NQ)
-Deamidation 18O (N)
-Dimethyl (KR)
-Gln->Ala
-Gln->Arg
-Gln->Asn
-Gln->Asp
-Gln->CamCys
-Gln->Cys
-Gln->Glu
-Gln->Gly
-Gln->His
-Gln->Lys
-Gln->Met
-Gln->Phe
-Gln->Pro
-Gln->pyro-Glu
-Gln->Ser
-Gln->Thr
-Gln->Trp
-Gln->Tyr
-Gln->Val
-Gln->Xle
-Glu->Ala
-Glu->Arg
-Glu->Asn
-Glu->Asp
-Glu->CamCys
-Glu->Cys
-Glu->Gln
-Glu->Gly
-Glu->His
-Glu->Lys
-Glu->Met
-Glu->Phe
-Glu->Pro
-Glu->pyro-Glu
-Glu->Ser
-Glu->Thr
-Glu->Trp
-Glu->Tyr
-Glu->Val
-Glu->Xle
-Gly->Ala
-Gly->Arg
-Gly->Asn
-Gly->Asp
-Gly->CamCys
-Gly->Cys
-Gly->Gln
-Gly->Glu
-Gly->His
-Gly->Lys
-Gly->Met
-Gly->Phe
-Gly->Pro
-Gly->Ser
-Gly->Thr
-Gly->Trp
-Gly->Tyr
-Gly->Val
-Gly->Xle
-GlyGly (K)
-His->Ala
-His->Arg
-His->Asn
-His->Asp
-His->CamCys
-His->Cys
-His->Gln
-His->Glu
-His->Gly
-His->Lys
-His->Met
-His->Phe
-His->Pro
-His->Ser
-His->Thr
-His->Trp
-His->Tyr
-His->Val
-His->Xle
-Lys->Ala
-Lys->Arg
-Lys->Asn
-Lys->Asp
-Lys->CamCys
-Lys->Cys
-Lys->Gln
-Lys->Glu
-Lys->Gly
-Lys->His
-Lys->Met
-Lys->Phe
-Lys->Pro
-Lys->Ser
-Lys->Thr
-Lys->Trp
-Lys->Tyr
-Lys->Val
-Lys->Xle
-Met->Ala
-Met->Arg
-Met->Asn
-Met->Asp
-Met->CamCys
-Met->Cys
-Met->Gln
-Met->Glu
-Met->Gly
-Met->His
-Met->Lys
-Met->Phe
-Met->Pro
-Met->Ser
-Met->Thr
-Met->Trp
-Met->Tyr
-Met->Val
-Met->Xle
-Methyl (KR)
-OHexNAc
-Phe->Ala
-Phe->Arg
-Phe->Asn
-Phe->Asp
-Phe->CamCys
-Phe->Cys
-Phe->Gln
-Phe->Glu
-Phe->Gly
-Phe->His
-Phe->Lys
-Phe->Met
-Phe->Pro
-Phe->Ser
-Phe->Thr
-Phe->Trp
-Phe->Tyr
-Phe->Val
-Phe->Xle
-Phospho (STY)
-Pro->Ala
-Pro->Arg
-Pro->Asn
-Pro->Asp
-Pro->CamCys
-Pro->Cys
-Pro->Gln
-Pro->Glu
-Pro->Gly
-Pro->His
-Pro->Lys
-Pro->Met
-Pro->Phe
-Pro->Ser
-Pro->Thr
-Pro->Trp
-Pro->Tyr
-Pro->Val
-Pro->Xle
-Pro5
-Pro6
-QQTGG (K)
-Ser->Ala
-Ser->Arg
-Ser->Asn
-Ser->Asp
-Ser->CamCys
-Ser->Cys
-Ser->Gln
-Ser->Glu
-Ser->Gly
-Ser->His
-Ser->Lys
-Ser->Met
-Ser->Phe
-Ser->Pro
-Ser->Thr
-Ser->Trp
-Ser->Tyr
-Ser->Val
-Ser->Xle
-Thr->Ala
-Thr->Arg
-Thr->Asn
-Thr->Asp
-Thr->CamCys
-Thr->Cys
-Thr->Gln
-Thr->Glu
-Thr->Gly
-Thr->His
-Thr->Lys
-Thr->Met
-Thr->Phe
-Thr->Pro
-Thr->Ser
-Thr->Trp
-Thr->Tyr
-Thr->Val
-Thr->Xle
-Trimethyl (K)
-Trp->Ala
-Trp->Arg
-Trp->Asn
-Trp->Asp
-Trp->CamCys
-Trp->Cys
-Trp->Gln
-Trp->Glu
-Trp->Gly
-Trp->His
-Trp->Lys
-Trp->Met
-Trp->Phe
-Trp->Pro
-Trp->Ser
-Trp->Thr
-Trp->Tyr
-Trp->Val
-Trp->Xle
-Tyr->Ala
-Tyr->Arg
-Tyr->Asn
-Tyr->Asp
-Tyr->CamCys
-Tyr->Cys
-Tyr->Gln
-Tyr->Glu
-Tyr->Gly
-Tyr->His
-Tyr->Lys
-Tyr->Met
-Tyr->Phe
-Tyr->Pro
-Tyr->Ser
-Tyr->Thr
-Tyr->Trp
-Tyr->Val
-Tyr->Xle
-Val->Ala
-Val->Arg
-Val->Asn
-Val->Asp
-Val->CamCys
-Val->Cys
-Val->Gln
-Val->Glu
-Val->Gly
-Val->His
-Val->Lys
-Val->Met
-Val->Phe
-Val->Pro
-Val->Ser
-Val->Thr
-Val->Trp
-Val->Tyr
-Val->Xle
-Xle->Ala
-Xle->Arg
-Xle->Asn
-Xle->Asp
-Xle->CamCys
-Xle->Cys
-Xle->Gln
-Xle->Glu
-Xle->Gly
-Xle->His
-Xle->Lys
-Xle->Met
-Xle->Phe
-Xle->Pro
-Xle->Ser
-Xle->Thr
-Xle->Trp
-Xle->Tyr
-Xle->Val

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_mods.loc.sample.default
--- a/maxquant_mods.loc.sample.default Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_mods.loc.sample.extended
--- a/maxquant_mods.loc.sample.extended Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1308 +0,0 @@\n-Acetyl (K)\n-Acetyl (Protein N-term)\n-Carbamidomethyl (C)\n-Oxidation (M)\n-Phospho (STY)\n-Arg6\n-Arg10\n-Lys4\n-Lys6\n-Lys8\n-GlyGly (K)\n-Methyl (KR)\n-Dimethyl (KR)\n-Trimethyl (K)\n-Pro5\n-Pro6\n-Glu->pyro-Glu\n-Gln->pyro-Glu\n-OHexNAc\n-DimethLys0\n-DimethNter0\n-DimethLys4\n-DimethNter4\n-DimethLys8\n-DimethNter8\n-18O\n-ICAT-0\n-ICAT-9\n-ICPL-Lys0\n-ICPL-Nter0\n-ICPL-Lys4\n-ICPL-Nter4\n-ICPL-Lys6\n-ICPL-Nter6\n-ICPL-Lys10\n-ICPL-Nter10\n-mTRAQ-Lys0\n-mTRAQ-Nter0\n-mTRAQ-Lys4\n-mTRAQ-Nter4\n-mTRAQ-Lys8\n-mTRAQ-Nter8\n-DimethLys2\n-DimethNter2\n-DimethLys6\n-DimethNter6\n-QQTGG (K)\n-Deamidation (N)\n-Deamidation 18O (N)\n-iTRAQ4plex-Nter114\n-iTRAQ4plex-Nter115\n-iTRAQ4plex-Nter116\n-iTRAQ4plex-Nter117\n-iTRAQ4plex-Lys114\n-iTRAQ4plex-Lys115\n-iTRAQ4plex-Lys116\n-iTRAQ4plex-Lys117\n-iTRAQ8plex-Nter113\n-iTRAQ8plex-Nter114\n-iTRAQ8plex-Nter115\n-iTRAQ8plex-Nter116\n-iTRAQ8plex-Nter117\n-iTRAQ8plex-Nter118\n-iTRAQ8plex-Nter119\n-iTRAQ8plex-Nter121\n-iTRAQ8plex-Lys113\n-iTRAQ8plex-Lys114\n-iTRAQ8plex-Lys115\n-iTRAQ8plex-Lys116\n-iTRAQ8plex-Lys117\n-iTRAQ8plex-Lys118\n-iTRAQ8plex-Lys119\n-iTRAQ8plex-Lys121\n-TMT2plex-Nter126\n-TMT2plex-Nter127\n-TMT2plex-Lys126\n-TMT2plex-Lys127\n-TMT6plex-Nter126\n-TMT6plex-Nter127\n-TMT6plex-Nter128\n-TMT6plex-Nter129\n-TMT6plex-Nter130\n-TMT6plex-Nter131\n-TMT6plex-Lys126\n-TMT6plex-Lys127\n-TMT6plex-Lys128\n-TMT6plex-Lys129\n-TMT6plex-Lys130\n-TMT6plex-Lys131\n-Deamidation (NQ)\n-Ala->Arg\n-Ala->Asn\n-Ala->Asp\n-Ala->Cys\n-Ala->Gln\n-Ala->Glu\n-Ala->Gly\n-Ala->His\n-Ala->Xle\n-Ala->Lys\n-Ala->Met\n-Ala->Phe\n-Ala->Pro\n-Ala->Ser\n-Ala->Thr\n-Ala->Trp\n-Ala->Tyr\n-Ala->Val\n-Arg->Ala\n-Arg->Asn\n-Arg->Asp\n-Arg->Cys\n-Arg->Gln\n-Arg->Glu\n-Arg->Gly\n-Arg->His\n-Arg->Lys\n-Arg->Met\n-Arg->Phe\n-Arg->Pro\n-Arg->Ser\n-Arg->Thr\n-Arg->Trp\n-Arg->Tyr\n-Arg->Val\n-Arg->Xle\n-Asn->Ala\n-Asn->Arg\n-Asn->Asp\n-Asn->Cys\n-Asn->Gln\n-Asn->Glu\n-Asn->Gly\n-Asn->His\n-Asn->Lys\n-Asn->Met\n-Asn->Phe\n-Asn->Pro\n-Asn->Ser\n-Asn->Thr\n-Asn->Trp\n-Asn->Tyr\n-Asn->Val\n-Asn->Xle\n-Asp->Ala\n-Asp->Arg\n-Asp->Asn\n-Asp->Cys\n-Asp->Gln\n-Asp->Glu\n-Asp->Gly\n-Asp->His\n-Asp->Lys\n-Asp->Met\n-Asp->Phe\n-Asp->Pro\n-Asp->Ser\n-Asp->Thr\n-Asp->Trp\n-Asp->Tyr\n-Asp->Val\n-Asp->Xle\n-Cys->Ala\n-Cys->Arg\n-Cys->Asn\n-Cys->Asp\n-Cys->Gln\n-Cys->Glu\n-Cys->Gly\n-Cys->His\n-Cys->Lys\n-Cys->Met\n-Cys->Phe\n-Cys->Pro\n-Cys->Ser\n-Cys->Thr\n-Cys->Trp\n-Cys->Tyr\n-Cys->Val\n-Cys->Xle\n-Gln->Ala\n-Gln->Arg\n-Gln->Asn\n-Gln->Asp\n-Gln->Cys\n-Gln->Glu\n-Gln->Gly\n-Gln->His\n-Gln->Lys\n-Gln->Met\n-Gln->Phe\n-Gln->Pro\n-Gln->Ser\n-Gln->Thr\n-Gln->Trp\n-Gln->Tyr\n-Gln->Val\n-Gln->Xle\n-Glu->Ala\n-Glu->Arg\n-Glu->Asn\n-Glu->Asp\n-Glu->Cys\n-Glu->Gln\n-Glu->Gly\n-Glu->His\n-Glu->Lys\n-Glu->Met\n-Glu->Phe\n-Glu->Pro\n-Glu->Ser\n-Glu->Thr\n-Glu->Trp\n-Glu->Tyr\n-Glu->Val\n-Glu->Xle\n-Gly->Ala\n-Gly->Arg\n-Gly->Asn\n-Gly->Asp\n-Gly->Cys\n-Gly->Gln\n-Gly->Glu\n-Gly->His\n-Gly->Lys\n-Gly->Met\n-Gly->Phe\n-Gly->Pro\n-Gly->Ser\n-Gly->Thr\n-Gly->Trp\n-Gly->Tyr\n-Gly->Val\n-Gly->Xle\n-His->Ala\n-His->Arg\n-His->Asn\n-His->Asp\n-His->Cys\n-His->Gln\n-His->Glu\n-His->Gly\n-His->Lys\n-His->Met\n-His->Phe\n-His->Pro\n-His->Ser\n-His->Thr\n-His->Trp\n-His->Tyr\n-His->Val\n-His->Xle\n-Lys->Ala\n-Lys->Arg\n-Lys->Asn\n-Lys->Asp\n-Lys->Cys\n-Lys->Gln\n-Lys->Glu\n-Lys->Gly\n-Lys->His\n-Lys->Met\n-Lys->Phe\n-Lys->Pro\n-Lys->Ser\n-Lys->Thr\n-Lys->Trp\n-Lys->Tyr\n-Lys->Val\n-Lys->Xle\n-Met->Ala\n-Met->Arg\n-Met->Asn\n-Met->Asp\n-Met->Cys\n-Met->Gln\n-Met->Glu\n-Met->Gly\n-Met->His\n-Met->Lys\n-Met->Phe\n-Met->Pro\n-Met->Ser\n-Met->Thr\n-Met->Trp\n-Met->Tyr\n-Met->Val\n-Met->Xle\n-Phe->Ala\n-Phe->Arg\n-Phe->Asn\n-Phe->Asp\n-Phe->Cys\n-Phe->Gln\n-Phe->Glu\n-Phe->Gly\n-Phe->His\n-Phe->Lys\n-Phe->Met\n-Phe->Pro\n-Phe->Ser\n-Phe->Thr\n-Phe->Trp\n-Phe->Tyr\n-Phe->Val\n-Phe->Xle\n-Pro->Ala\n-Pro->Arg\n-Pro->Asn\n-Pro->Asp\n-Pro->Cys\n-Pro->Gln\n-Pro->Glu\n-Pro->Gly\n-Pro->His\n-Pro->Lys\n-Pro->Met\n-Pro->Phe\n-Pro->Ser\n-Pro->Thr\n-Pro->Trp\n-Pro->Tyr\n-Pro->Val\n-Pro->Xle\n-Ser->Ala\n-Ser->Arg\n-Ser->Asn\n-Ser->Asp\n-Ser->Cys\n-Ser->Gln\n-Ser->Glu\n-Ser->Gly\n-Ser->His\n-Ser->Lys\n-Ser->Met\n-Ser->Phe\n-Ser->Pro\n-Ser->Thr\n-Ser->Trp\n-Ser->Tyr\n-Ser->Val\n-Ser->Xle\n-Thr->Ala\n-Thr->Arg\n-Thr->Asn\n-Thr->Asp\n-Thr->Cys\n-Thr->Gln\n-Thr->Glu\n-Thr->Gly\n-Thr->His\n-Thr->Lys\n-Thr-'..b'r->Pro (T) [Unimod]\n-Thr->Met (T) [Unimod]\n-Thr->Ile (T) [Unimod]\n-Thr->Arg (T) [Unimod]\n-Val->Phe (V) [Unimod]\n-Val->Ala (V) [Unimod]\n-Val->Glu (V) [Unimod]\n-Val->Met (V) [Unimod]\n-Val->Asp (V) [Unimod]\n-Val->Ile (V) [Unimod]\n-Val->Gly (V) [Unimod]\n-Trp->Ser (W) [Unimod]\n-Trp->Cys (W) [Unimod]\n-Trp->Arg (W) [Unimod]\n-Trp->Gly (W) [Unimod]\n-Trp->Leu (W) [Unimod]\n-Tyr->Phe (Y) [Unimod]\n-Tyr->Ser (Y) [Unimod]\n-Tyr->Asn (Y) [Unimod]\n-Tyr->His (Y) [Unimod]\n-Tyr->Asp (Y) [Unimod]\n-Tyr->Cys (Y) [Unimod]\n-NA-LNO2 (C) [Unimod]\n-NA-LNO2 (H) [Unimod]\n-NA-OA-NO2 (C) [Unimod]\n-NA-OA-NO2 (H) [Unimod]\n-ICPL:2H(4) (N-term) [Unimod]\n-ICPL:2H(4) (N-term) [Unimod]\n-ICPL:2H(4) (K) [Unimod]\n-iTRAQ8plex (Y) [Unimod]\n-iTRAQ8plex (N-term) [Unimod]\n-iTRAQ8plex (K) [Unimod]\n-Label:13C(6)15N(1) (I) [Unimod]\n-Label:13C(6)15N(1) (L) [Unimod]\n-Label:2H(9)13C(6)15N(2) (K) [Unimod]\n-HNE-Delta:H(2)O (K) [Unimod]\n-HNE-Delta:H(2)O (H) [Unimod]\n-HNE-Delta:H(2)O (C) [Unimod]\n-4-ONE (K) [Unimod]\n-4-ONE (H) [Unimod]\n-4-ONE (C) [Unimod]\n-O-Dimethylphosphate (Y) [Unimod]\n-O-Dimethylphosphate (T) [Unimod]\n-O-Dimethylphosphate (S) [Unimod]\n-O-Methylphosphate (Y) [Unimod]\n-O-Methylphosphate (T) [Unimod]\n-O-Methylphosphate (S) [Unimod]\n-O-Diethylphosphate (Y) [Unimod]\n-O-Diethylphosphate (T) [Unimod]\n-O-Diethylphosphate (S) [Unimod]\n-O-Ethylphosphate (Y) [Unimod]\n-O-Ethylphosphate (T) [Unimod]\n-O-Ethylphosphate (S) [Unimod]\n-O-pinacolylmethylphosphonate (Y) [Unimod]\n-O-pinacolylmethylphosphonate (T) [Unimod]\n-O-pinacolylmethylphosphonate (S) [Unimod]\n-Methylphosphonate (Y) [Unimod]\n-Methylphosphonate (T) [Unimod]\n-Methylphosphonate (S) [Unimod]\n-O-Isopropylmethylphosphonate (Y) [Unimod]\n-O-Isopropylmethylphosphonate (T) [Unimod]\n-O-Isopropylmethylphosphonate (S) [Unimod]\n-iTRAQ8plex:13C(6)15N(2) (Y) [Unimod]\n-iTRAQ8plex:13C(6)15N(2) (N-term) [Unimod]\n-iTRAQ8plex:13C(6)15N(2) (K) [Unimod]\n-DTT_ST (S) [Unimod]\n-DTT_ST (T) [Unimod]\n-Ethanolamine (D) [Unimod]\n-Ethanolamine (C-term) [Unimod]\n-Ethanolamine (E) [Unimod]\n-TMT6plex (K) [Unimod]\n-TMT6plex (N-term) [Unimod]\n-DTT_C (C) [Unimod]\n-TMT2plex (N-term) [Unimod]\n-TMT2plex (K) [Unimod]\n-TMT (N-term) [Unimod]\n-TMT (K) [Unimod]\n-ExacTagThiol (C) [Unimod]\n-ExacTagAmine (K) [Unimod]\n-NO_SMX_SEMD (C) [Unimod]\n-4-ONE+Delta:H(-2)O(-1) (K) [Unimod]\n-4-ONE+Delta:H(-2)O(-1) (H) [Unimod]\n-4-ONE+Delta:H(-2)O(-1) (C) [Unimod]\n-NO_SMX_SMCT (C) [Unimod]\n-NO_SMX_SIMD (C) [Unimod]\n-Malonyl (C) [Unimod]\n-Malonyl (S) [Unimod]\n-3sulfo (N-term) [Unimod]\n-trifluoro (L) [Unimod]\n-TNBS (N-term) [Unimod]\n-TNBS (K) [Unimod]\n-Biotin-phenacyl (C) [Unimod]\n-Biotin-phenacyl (H) [Unimod]\n-Biotin-phenacyl (S) [Unimod]\n-DTT_C:2H(6) (C) [Unimod]\n-lapachenole (C) [Unimod]\n-Label:13C(5) (P) [Unimod]\n-maleimide (K) [Unimod]\n-maleimide (C) [Unimod]\n-DTT_ST:2H(6) (T) [Unimod]\n-DTT_ST:2H(6) (S) [Unimod]\n-Met-loss (M) [Unimod]\n-Met-loss+Acetyl (M) [Unimod]\n-Menadione-HQ (K) [Unimod]\n-Menadione-HQ (C) [Unimod]\n-Carboxymethyl:13C(2) (C) [Unimod]\n-NEM:2H(5) (C) [Unimod]\n-Gly-loss+Amide (G) [Unimod]\n-TMPP-Ac (N-term) [Unimod]\n-Label:13C(6)+GlyGly (K) [Unimod]\n-Arg->Npo (R) [Unimod]\n-Label:2H(4)+Acetyl (K) [Unimod]\n-Pentylamine (Q) [Unimod]\n-PentylamineBiotin (Q) [Unimod]\n-Dihydroxyimidazolidine (R) [Unimod]\n-DFDNB (Q) [Unimod]\n-DFDNB (N) [Unimod]\n-DFDNB (R) [Unimod]\n-DFDNB (K) [Unimod]\n-Cy3b-maleimide (C) [Unimod]\n-AEC-MAEC:2H(4) (S) [Unimod]\n-AEC-MAEC:2H(4) (T) [Unimod]\n-BMOE (C) [Unimod]\n-Biotin-PEO4-hydrazide (C-term) [Unimod]\n-Label:13C(6)+Acetyl (K) [Unimod]\n-Label:13C(6)15N(2)+Acetyl (K) [Unimod]\n-EQIGG (K) [Unimod]\n-cGMP (C) [Unimod]\n-cGMP+RMP-loss (C) [Unimod]\n-Arg2PG (R) [Unimod]\n-Label:2H(4)+GlyGly (K) [Unimod]\n-Label:13C(8)15N(2) (R) [Unimod]\n-Label:13C(1)2H(3) (M) [Unimod]\n-ZGB (K) [Unimod]\n-ZGB (N-term) [Unimod]\n-MG-H1 (R) [Unimod]\n-G-H1 (R) [Unimod]\n-Label:13C(6)15N(2)+GlyGly (K) [Unimod]\n-ICPL:13C(6)2H(4) (N-term) [Unimod]\n-ICPL:13C(6)2H(4) (K) [Unimod]\n-ICPL:13C(6)2H(4) (N-term) [Unimod]\n-QQQTGG (K) [Unimod]\n-QEQTGG (K) [Unimod]\n-Bodipy (C) [Unimod]\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_proteases.loc
--- a/maxquant_proteases.loc Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,27 +0,0 @@
-Trypsin
-Arg-C
-Asp-N
-Asp-N_ambic
-Chymotrypsin
-CNBr
-CNBr+Trypsin
-Formic_acid
-Lys-C
-Lys-C/P
-PepsinA
-Tryp-CNBr
-TrypChymo
-Trypsin/P
-Trypsin/P+DP
-V8-DE
-V8-E
-semiTrypsin
-LysC+AspN
-Lys-C/P+DP
-Trypsin/P + Asp-N
-Asp-C
-Trypsin/P+Asp-C
-SemiLys
-SemiGluC
-LysC/P+AspC
-GluC

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_proteases.loc.sample
--- a/maxquant_proteases.loc.sample Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r d4b6c9eae635 -r 8bac3cc5c5de maxquant_wrapper.py
--- a/maxquant_wrapper.py Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,787 +0,0 @@\n-#!/usr/bin/env python\n-import optparse\n-import os\n-import shutil\n-import sys\n-import tempfile\n-import subprocess\n-import logging\n-from string import Template\n-from xml.sax.saxutils import escape\n-import xml.etree.ElementTree as ET\n-\n-log = logging.getLogger(__name__)\n-\n-DEBUG = True\n-\n-working_directory = os.getcwd()\n-tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n-tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n-\n-\n-def stop_err(msg):\n- sys.stderr.write("%s\\n" % msg)\n- sys.exit()\n-\n-\n-def read_stderr():\n- stderr = \'\'\n- if(os.path.exists(tmp_stderr_name)):\n- with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read(buffsize)\n- if not stderr or len(stderr) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- return stderr\n-\n-\n-def execute(command, stdin=None):\n- try:\n- with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n- with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n- proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n- returncode = proc.wait()\n- if returncode != 0:\n- raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n- finally:\n- print open(tmp_stderr_name, "r").read(64000)\n- print open(tmp_stdout_name, "r").read(64000)\n-\n-\n-def delete_file(path):\n- if os.path.exists(path):\n- try:\n- os.remove(path)\n- except:\n- pass\n-\n-\n-def delete_directory(directory):\n- if os.path.exists(directory):\n- try:\n- shutil.rmtree(directory)\n- except:\n- pass\n-\n-\n-def symlink(source, link_name):\n- import platform\n- if platform.system() == \'Windows\':\n- try:\n- import win32file\n- win32file.CreateSymbolicLink(source, link_name, 1)\n- except:\n- shutil.copy(source, link_name)\n- else:\n- os.symlink(source, link_name)\n-\n-\n-def copy_to_working_directory(data_file, relative_path):\n- if os.path.abspath(data_file) != os.path.abspath(relative_path):\n- shutil.copy(data_file, relative_path)\n- return relative_path\n-\n-\n-def __main__():\n- run_script()\n-\n-\n-## Lock File Stuff\n-## http://www.evanfosmark.com/2009/01/cross-platform-file-locking-support-in-python/\n-import os\n-import time\n-import errno\n-\n-\n-class FileLockException(Exception):\n- pass\n-\n-\n-class FileLock(object):\n- """ A file locking mechanism that has context-manager support so\n- you can use it in a with statement. This should be relatively cross\n- compatible as it doesn\'t rely on msvcrt or fcntl for the locking.\n- """\n-\n- def __init__(self, file_name, timeout=10, delay=.05):\n- """ Prepare the file locker. Specify the file to lock and optionally\n- the maximum timeout and the delay between each attempt to lock.\n- """\n- self.is_locked = False\n- self.lockfile = os.path.join(os.getcwd(), "%s.lock" % file_name)\n- self.file_name = file_name\n- self.timeout = timeout\n- self.delay = delay\n-\n- def acquire(self):\n- """ Acquire the lock, if possible. If the lock is in use, it check again\n- every `wait` seconds. It does this until it either gets the lock or\n- exceeds `timeout` number of seconds, in which case it throws\n- an exception.\n- """\n- start_time = time.time()\n- while True:\n- try:\n- self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)\n- break\n- except OSError as e:\n- if e.errno != errno.'..b'_option("--msms_connection", default="false")\n- parser.add_option("--ibaq", default="false")\n- parser.add_option("--msms_recalibration", default="false")\n- parser.add_option("--ibaq_log_fit", default="true")\n- parser.add_option("--razor_protein_fdr", default="true")\n- parser.add_option("--calc_sequence_tags", default="false")\n- parser.add_option("--de_novo_var_mods", default="true")\n- parser.add_option("--mass_difference_search", default="false")\n- parser.add_option("--min_pep_len", default="7")\n- parser.add_option("--peptide_fdr", default="0.01")\n- parser.add_option("--peptide_pep", default="1")\n- parser.add_option("--protein_fdr", default="0.01")\n- parser.add_option("--site_fdr", default="0.01")\n- parser.add_option("--min_peptide_length_for_unspecific_search", default="8")\n- parser.add_option("--max_peptide_length_for_unspecific_search", default="25")\n- parser.add_option("--use_norm_ratios_for_occupancy", default="true")\n- parser.add_option("--min_peptides", default="1")\n- parser.add_option("--min_razor_peptides", default="1")\n- parser.add_option("--min_unique_peptides", default="0")\n- parser.add_option("--use_counterparts", default="false")\n- parser.add_option("--min_ratio_count", default="2")\n- parser.add_option("--lfq_min_ratio_count", default="2")\n- parser.add_option("--calc_peak_properties", default="false")\n- parser.add_option("--use_original_precursor_mz", default="false")\n- parser.add_option("--multi_modification_search", default="false")\n- parser.add_option("--lcms_run_type", default="0")\n- parser.add_option("--reporter_type", default=None)\n- parser.add_option("--output_mqpar", default=None)\n- text_outputs = {\n- "aif_msms": "aifMsms",\n- "all_peptides": "allPeptides",\n- "evidence": "evidence",\n- "modification_specific_peptides": "modificationSpecificPeptides",\n- "msms": "msms",\n- "msms_scans": "msmsScans",\n- "mz_range": "mzRange",\n- "parameters": "parameters",\n- "peptides": "peptides",\n- "protein_groups": "proteinGroups",\n- "sim_peptides": "simPeptides",\n- "sim_scans": "simScans",\n- "summary": "summary"\n- }\n- for output in text_outputs.keys():\n- parser.add_option("--output_%s" % output, default=None)\n-\n- parser.add_option("--variable_mods", default="Oxidation (M),Acetyl (Protein N-term)")\n- parser.add_option("--restrict_mods", default="Oxidation (M),Acetyl (Protein N-term)")\n- parser.add_option("--fixed_mods", default="Carbamidomethyl (C)")\n-\n- add_fragment_options(parser)\n-\n- (options, args) = parser.parse_args()\n- options.restrict_mods = split_mods(options.restrict_mods)\n- options.fixed_mods = split_mods(options.fixed_mods)\n- options.variable_mods = split_mods(options.variable_mods)\n-\n- update_fragment_settings(options)\n-\n- raw_file_info = setup_inputs(options.input_groups)\n- properties = get_properties(options)\n- properties["raw_file_info"] = raw_file_info\n- properties["isobaric_labels"] = build_isobaric_labels(options.reporter_type)\n- set_group_params(properties, options)\n- driver_contents = Template(TEMPLATE).substitute(properties)\n- open("mqpar.xml", "w").write(driver_contents)\n- print driver_contents\n- execute("MaxQuantCmd.exe mqpar.xml %d" % options.num_cores)\n- for key, basename in text_outputs.iteritems():\n- attribute = "output_%s" % key\n- destination = getattr(options, attribute, None)\n- if destination:\n- source = os.path.join("combined", "txt", "%s.txt" % basename)\n- shutil.copy(source, destination)\n- output_mqpar = options.output_mqpar\n- if output_mqpar:\n- shutil.copy("mqpar.xml", output_mqpar)\n-\n-if __name__ == \'__main__\':\n- __main__()\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de modifications.xml
--- a/modifications.xml Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2580 +0,0 @@\n-\xef\xbb\xbf<?xml version="1.0" encoding="utf-8"?>\r\n-<modifications xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r\n- <modification index="0" title="Acetyl (K)" description="Acetylation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(2) H(2) O" create_date="2010-01-19T13:25:24.82357+01:00" last_modified_date="2010-01-19T14:15:40.2445414+01:00" user="neuhause" multi_modification="false">\r\n- <position>notCterm</position>\r\n- <modification_site index="0" site="K">\r\n- <diagnostic_collection>\r\n- <diagnostic name="acK*" shortname="acK*" composition="C(7) H(11) O N" />\r\n- <diagnostic name="acK" shortname="acK" composition="C(7) H(14) O N(2)" />\r\n- </diagnostic_collection>\r\n- </modification_site>\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="1" title="Acetyl (Protein N-term)" description="Acetylation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(2) H(2) O" create_date="2010-01-19T14:27:34.5843488+01:00" last_modified_date="2010-01-19T14:28:09.7383488+01:00" user="neuhause" multi_modification="false">\r\n- <position>proteinNterm</position>\r\n- <modification_site index="0" site="-" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="2" title="Carbamidomethyl (C)" description="Iodoacetamide derivative" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(2) H(3) N O" create_date="2010-01-19T15:54:02.1976309+01:00" last_modified_date="2010-01-19T15:55:13.1353165+01:00" user="neuhause" multi_modification="false">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="C" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="3" title="Oxidation (M)" description="Oxidation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="O " create_date="2010-01-19T14:29:05.2191728+01:00" last_modified_date="2010-01-19T20:38:21.9609829+01:00" user="neuhause" multi_modification="false">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="M" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="4" title="Phospho (STY)" description="Phosphorylation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="H O(3) P" create_date="2010-01-19T14:34:50.0721008+01:00" last_modified_date="2010-01-19T20:39:28.1471599+01:00" user="neuhause" multi_modification="false">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="S">\r\n- <neutralloss_collection>\r\n- <neutralloss name="H(3) O(4) P" shortname="H3 O4 P" composition="H(3) O(4) P" />\r\n- </neutralloss_collection>\r\n- </modification_site>\r\n- <modification_site index="1" site="T">\r\n- <neutralloss_collection>\r\n- <neutralloss name="H(3) O(4) P" shortname="H3 O4 P" composition="H(3) O(4) P" />\r\n- </neutralloss_collection>\r\n- </modification_site>\r\n- <modification_site index="2" site="Y">\r\n- <diagnostic_collection>\r\n- <diagnostic name="C(8) H(10) O(4) N P" shortname="pY" composition="C(8) H(10) O(4) N P" />\r\n- </diagnostic_collection>\r\n- </modification_site>\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="5" title="Arg6" description="Arginine-13C6 (R-13C6)" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="Cx(6) C(-6)" create_date="2010-01-19T14:37:21.2757206+01:00" last_modified_date="2010-01-23T19:17:45.328125+01:00" user="cox" multi_modification="false">\r\n- <position>anywhere</position>\r\n- <mod'..b'porterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="S H(3) C(2) N" create_date="2012-02-12T13:02:29.9546199+01:00" last_modified_date="2012-02-12T14:27:05.7229376+01:00" user="cox" multi_modification="true">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="S" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="463" title="Thr->CamCys" description="Thr->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="S H C N" create_date="2012-02-12T13:02:38.5970351+01:00" last_modified_date="2012-02-12T14:27:34.2241876+01:00" user="cox" multi_modification="true">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="T" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="464" title="Trp->CamCys" description="Trp->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="H(-2) C(-6) S O" create_date="2012-02-12T13:02:44.7434459+01:00" last_modified_date="2012-02-12T14:27:57.3434282+01:00" user="cox" multi_modification="true">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="W" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="465" title="Tyr->CamCys" description="Tyr->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-4) H(-1) S N" create_date="2012-02-12T13:02:53.7134616+01:00" last_modified_date="2012-02-12T14:28:23.6450744+01:00" user="cox" multi_modification="true">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="Y" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="466" title="Val->CamCys" description="Val->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="H(-1) S N O" create_date="2012-02-12T13:02:58.2686696+01:00" last_modified_date="2012-02-12T14:28:51.5067234+01:00" user="cox" multi_modification="true">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="V" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="467" title="Xle->CamCys" description="Leu/Ile->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-1) H(-3) S N O" create_date="2012-02-12T13:03:06.2714837+01:00" last_modified_date="2012-02-12T14:29:18.5727709+01:00" user="cox" multi_modification="true">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="I" />\r\n- <modification_site index="1" site="L" />\r\n- <type>standard</type>\r\n- </modification>\r\n- <modification index="468" title="Leu7" description="Leucine-13C6 15N1" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-6) Cx(6) N(-1) Nx" create_date="2012-03-14T11:27:13.8771423+01:00" last_modified_date="2012-03-14T11:30:52.8703269+01:00" user="cox" multi_modification="false">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="L" />\r\n- <type>label</type>\r\n- </modification>\r\n- <modification index="469" title="Ile7" description="Isoleucine-13C6 15N1" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-6) Cx(6) N(-1) Nx" create_date="2012-06-11T21:21:24.4946343+02:00" last_modified_date="2012-06-11T21:21:24.4946343+02:00" user="cox" multi_modification="false">\r\n- <position>anywhere</position>\r\n- <modification_site index="0" site="I" />\r\n- <type>label</type>\r\n- </modification>\r\n-</modifications>\n\\ No newline at end of file\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de mqparam.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mqparam.py Sat Jul 20 05:01:05 2019 -0400

[

b'@@ -0,0 +1,349 @@\n+"""\n+Create a project-specific MaxQuant parameter file.\n+\n+TODO: check validity of parsed experimental design template\n+ add support for parameter groups\n+ add reporter ion MS2\n+ add label free quantification\n+ don\'t hardcode parse rules for fasta files\n+\n+Author: Damian Glaetzer <d.glaetzer@mailbox.org>\n+"""\n+\n+import ntpath\n+import os\n+import re\n+import xml.etree.ElementTree as ET\n+from itertools import zip_longest\n+from xml.dom import minidom\n+\n+\n+class MQParam:\n+ """Represents a mqpar.xml and provides methods to modify\n+ some of its parameters.\n+ """\n+\n+ fasta_template = """<FastaFileInfo>\n+ <fastaFilePath></fastaFilePath>\n+ <identifierParseRule></identifierParseRule>\n+ <descriptionParseRule></descriptionParseRule>\n+ <taxonomyParseRule></taxonomyParseRule>\n+ <variationParseRule></variationParseRule>\n+ <modificationParseRule></modificationParseRule>\n+ <taxonomyId></taxonomyId>\n+ </FastaFileInfo>"""\n+\n+ def __init__(self, mqpar_out, mqpar_in, exp_design,\n+ substitution_rx=r\'[^\\s\\S]\'): # no sub by default\n+ """Initialize MQParam class. mqpar_in can either be a template\n+ or a already suitable mqpar file.\n+ >>> t = MQParam("test", \'./test-data/template.xml\', None)\n+ >>> t.root.tag\n+ \'MaxQuantParams\'\n+ >>> (t.root.find(\'maxQuantVersion\')).text\n+ \'1.6.3.4\'\n+ """\n+\n+ self.orig_mqpar = mqpar_in\n+ self.exp_design = exp_design\n+ self.mqpar_out = mqpar_out\n+ self.root = ET.parse(mqpar_in).getroot()\n+ self.version = self.root.find(\'maxQuantVersion\').text\n+ # regex for substitution of certain file name characters\n+ self.substitution_rx = substitution_rx\n+\n+ @staticmethod\n+ def _add_child(el, name, text, attrib=None):\n+ """Add a child element to an element.\n+\n+ >>> t = MQParam("test", \'./test-data/template.xml\', None)\n+ >>> MQParam._add_child(t.root, "test", "test")\n+ >>> t.root.find(\'test\').text == "test"\n+ True\n+ """\n+\n+ child = ET.SubElement(el, name, attrib=attrib if attrib else {})\n+ child.text = str(text)\n+\n+ def _make_exp_design(self, infiles):\n+ """Create a dict representing an experimental design from\n+ an experimental design template and a list of input files.\n+ If the experimental design template is None, create a default\n+ design with one experiment for each input file, no fractions and\n+ parameter group 0 for all files.\n+ >>> t2 = MQParam("test", \'./test-data/template.xml\', \\\n+ \'./test-data/two/exp_design_template.txt\')\n+ >>> design = t2._make_exp_design([\'./test-data/BSA_min_21.mzXML\', \\\n+ \'./test-data/BSA_min_22.mzXML\'])\n+ >>> design[\'Name\']\n+ [\'./test-data/BSA_min_21.mzXML\', \'./test-data/BSA_min_22.mzXML\']\n+ >>> design[\'Fraction\']\n+ [\'1\', \'2\']\n+ """\n+ design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment")}\n+ if not self.exp_design:\n+ design["Name"] = infiles\n+ design["Fraction"] = (\'32767\',) * len(infiles)\n+ design["Experiment"] = [os.path.split(f)[1] for f in infiles]\n+ design["PTM"] = (\'False\',) * len(infiles)\n+ else:\n+ with open(self.exp_design) as design_file:\n+ index_line = design_file.readline().strip()\n+ index = []\n+ for i in index_line.split(\'\\t\'):\n+ if i in design:\n+ index.append(i)\n+ else:\n+ raise Exception("Invalid comlumn index in experimental"\n+ + " design template: {}".format(i))\n+ for line in design_file:\n+ row = line.strip().split(\'\\t\')\n+ for e, i in zip_longest(row, index):\n+ '..b'EdgesPerNode\',\n+ \'lfq_avg_edges_per_node\':\n+ \'.parameterGroups/parameterGroup/lfqAvEdgesPerNode\',\n+ \'lfq_min_ratio_count\':\n+ \'.parameterGroups/parameterGroup/lfqMinRatioCount\'}\n+\n+ if key in simple_params:\n+ node = self.root.find(simple_params[key])\n+ if node is None:\n+ raise ValueError(\'Element {} not found in parameter file\'\n+ .format(simple_params[key]))\n+ node.text = str(value)\n+ else:\n+ raise ValueError("Parameter not found.")\n+\n+ def set_silac(self, light_mods, medium_mods, heavy_mods):\n+ """Set label modifications.\n+ >>> t1 = MQParam(\'test\', \'./test-data/template.xml\', None)\n+ >>> t1.set_silac(None, (\'test1\', \'test2\'), None)\n+ >>> t1.root.find(\'.parameterGroups/parameterGroup/maxLabeledAa\').text\n+ \'2\'\n+ >>> t1.root.find(\'.parameterGroups/parameterGroup/multiplicity\').text\n+ \'3\'\n+ >>> t1.root.find(\'.parameterGroups/parameterGroup/labelMods\')[1].text\n+ \'test1;test2\'\n+ >>> t1.root.find(\'.parameterGroups/parameterGroup/labelMods\')[2].text\n+ \'\'\n+ """\n+ multiplicity = 3 if medium_mods else 2 if heavy_mods else 1\n+ max_label = str(max(len(light_mods) if light_mods else 0,\n+ len(medium_mods) if medium_mods else 0,\n+ len(heavy_mods) if heavy_mods else 0))\n+ multiplicity_node = self.root.find(\'.parameterGroups/parameterGroup/\'\n+ + \'multiplicity\')\n+ multiplicity_node.text = str(multiplicity)\n+ max_label_node = self.root.find(\'.parameterGroups/parameterGroup/\'\n+ + \'maxLabeledAa\')\n+ max_label_node.text = max_label\n+\n+ node = self.root.find(\'.parameterGroups/parameterGroup/labelMods\')\n+ node[0].text = \';\'.join(light_mods) if light_mods else \'\'\n+ if multiplicity == 3:\n+ MQParam._add_child(node, name=\'string\', text=\';\'.join(medium_mods))\n+ if multiplicity > 1:\n+ MQParam._add_child(node, name=\'string\',\n+ text=\';\'.join(heavy_mods) if heavy_mods else \'\')\n+\n+ def set_list_params(self, key, vals):\n+ """Set a list parameter.\n+ >>> t = MQParam(None, \'./test-data/template.xml\', None)\n+ >>> t.set_list_params(\'proteases\', (\'test 1\', \'test 2\'))\n+ >>> len(t.root.find(\'.parameterGroups/parameterGroup/enzymes\'))\n+ 2\n+ >>> t.set_list_params(\'var_mods\', (\'Oxidation (M)\', ))\n+ >>> var_mods = \'.parameterGroups/parameterGroup/variableModifications\'\n+ >>> t.root.find(var_mods)[0].text\n+ \'Oxidation (M)\'\n+ """\n+\n+ params = {\'var_mods\':\n+ \'.parameterGroups/parameterGroup/variableModifications\',\n+ \'fixed_mods\':\n+ \'.parameterGroups/parameterGroup/fixedModifications\',\n+ \'proteases\':\n+ \'.parameterGroups/parameterGroup/enzymes\'}\n+\n+ if key in params:\n+ node = self.root.find(params[key])\n+ if node is None:\n+ raise ValueError(\'Element {} not found in parameter file\'\n+ .format(params[key]))\n+ node.clear()\n+ node.tag = params[key].split(\'/\')[-1]\n+ for e in vals:\n+ MQParam._add_child(node, name=\'string\', text=e)\n+ else:\n+ raise ValueError("Parameter {} not found.".format(key))\n+\n+ def write(self):\n+ rough_string = ET.tostring(self.root, \'utf-8\', short_empty_elements=False)\n+ reparsed = minidom.parseString(rough_string)\n+ pretty = reparsed.toprettyxml(indent="\\t")\n+ even_prettier = re.sub(r"\\n\\s+\\n", r"\\n", pretty)\n+ with open(self.mqpar_out, \'w\') as f:\n+ print(even_prettier, file=f)\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de mqwrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mqwrapper.py Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,148 @@
+"""
+Run MaxQuant on a modified mqpar.xml.
+Use maxquant conda package.
+TODO: add support for parameter groups
+
+Authors: Damian Glaetzer <d.glaetzer@mailbox.org>
+
+based on the maxquant galaxy tool by John Chilton:
+https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
+"""
+
+import argparse
+import os
+import shutil
+import subprocess
+
+import mqparam
+
+# build parser
+parser = argparse.ArgumentParser()
+
+# input, special outputs and others
+other_args = ('raw_files', 'mzxml_files', 'fasta_files',
+              'description_parse_rule', 'identifier_parse_rule',
+              'exp_design', 'output_all',
+              'mqpar_out', 'infile_names', 'mzTab',
+              'version', 'substitution_rx')
+
+# txt result files
+txt_output = ('evidence', 'msms', 'parameters',
+              'peptides', 'proteinGroups', 'allPeptides',
+              'libraryMatch', 'matchedFeatures',
+              'modificationSpecificPeptides', 'ms3Scans',
+              'msmsScans', 'mzRange', 'peptideSection',
+              'summary')
+
+# arguments for mqparam
+## global
+global_flags = ('calc_peak_properties',
+                'write_mztab',
+                'ibaq',
+                'ibaq_log_fit',
+                'separate_lfq',
+                'lfq_stabilize_large_ratios',
+                'lfq_require_msms',
+                'advanced_site_intensities',
+                'match_between_runs')
+
+global_simple_args = ('min_unique_pep',
+                      'num_threads',
+                      'min_peptide_len',
+                      'max_peptide_mass')
+
+## parameter group specific
+param_group_flags = ('lfq_skip_norm',)
+
+param_group_simple_args = ('missed_cleavages',
+                           'lfq_mode',
+                           'lfq_min_edges_per_node',
+                           'lfq_avg_edges_per_node',
+                           'lfq_min_ratio_count')
+
+param_group_silac_args = ('light_mods', 'medium_mods', 'heavy_mods')
+
+list_args = ('fixed_mods', 'var_mods', 'proteases')
+
+arguments = ['--' + el for el in (txt_output
+                                  + global_simple_args
+                                  + param_group_simple_args
+                                  + list_args
+                                  + param_group_silac_args
+                                  + other_args)]
+
+flags = ['--' + el for el in global_flags + param_group_flags]
+
+for arg in arguments:
+    parser.add_argument(arg)
+for flag in flags:
+    parser.add_argument(flag, action="store_true")
+
+args = vars(parser.parse_args())
+
+# link infile datasets to names with correct extension
+# for maxquant to accept them
+files = (args['raw_files'] if args['raw_files']
+         else args['mzxml_files']).split(',')
+ftype = ".thermo.raw" if args['raw_files'] else ".mzXML"
+filenames = args['infile_names'].split(',')
+fnames_with_ext = [(a if a.endswith(ftype)
+                    else os.path.splitext(a)[0] + ftype)
+                   for a in filenames]
+
+for f, l in zip(files, fnames_with_ext):
+    os.link(f, l)
+
+# build mqpar.xml
+mqpar_in = os.path.join(os.getcwd(), 'mqpar.xml')
+subprocess.run(('maxquant', '-c', mqpar_in))
+mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in
+
+
+exp_design = args['exp_design'] if args['exp_design'] != 'None' else None
+m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design,
+                    substitution_rx=args['substitution_rx'])
+if m.version != args['version']:
+    raise Exception('mqpar version is ' + m.version +
+                    '. Tool uses version {}.'.format(args['version']))
+
+# modify parameters, interactive mode if no mqpar_in was specified
+m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], True)
+m.add_fasta_files(args['fasta_files'].split(','),
+                  identifier=args['identifier_parse_rule'],
+                  description=args['description_parse_rule'])
+
+for e in (global_simple_args
+          + param_group_simple_args
+          + global_flags
+          + param_group_flags):
+    if args[e]:
+        m.set_simple_param(e, args[e])
+
+for e in list_args:
+    if args[e]:
+        m.set_list_params(e, args[e].split(','))
+
+if args['light_mods'] or args['medium_mods'] or args['heavy_mods']:
+    m.set_silac(args['light_mods'].split(',') if args['light_mods'] else None,
+                args['medium_mods'].split(',') if args['medium_mods'] else None,
+                args['heavy_mods'].split(',') if args['heavy_mods'] else None)
+
+m.write()
+
+# build and run MaxQuant command
+cmd = ['maxquant', mqpar_out]
+
+subprocess.run(cmd, check=True, cwd='./')
+
+# copy results to galaxy database
+for el in txt_output:
+    destination = args[el]
+    source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el))
+    if destination != 'None' and os.path.isfile(source):
+        shutil.copy(source, destination)
+
+if args['mzTab'] != 'None':
+    source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab")
+    if os.path.isfile(source):
+        shutil.copy(source, args['mzTab'])

diff -r d4b6c9eae635 -r 8bac3cc5c5de proteases.xml
--- a/proteases.xml Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?><proteases xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><protease name="Trypsin" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="P" /></protease><protease name="Arg-C" semispecific="false"><rule index="1" sense="C-Term" cleave="R" restrict="P" /></protease><protease name="Asp-N" semispecific="false"><rule index="1" sense="N-Term" cleave="D" restrict="" /></protease><protease name="Asp-N_ambic" semispecific="false"><rule index="1" sense="N-Term" cleave="DE" restrict="" /></protease><protease name="Chymotrypsin" semispecific="false"><rule index="1" sense="C-Term" cleave="FLWY" restrict="P" /></protease><protease name="CNBr" semispecific="false"><rule index="1" sense="C-Term" cleave="M" restrict="" /></protease><protease name="CNBr+Trypsin" semispecific="false"><rule index="1" sense="C-Term" cleave="M" restrict="" /><rule index="2" sense="C-Term" cleave="KR" restrict="P" /></protease><protease name="Formic_acid" semispecific="false"><rule index="1" sense="C-Term" cleave="D" restrict="" /></protease><protease name="Lys-C" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="P" /></protease><protease name="Lys-C/P" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="" /></protease><protease name="PepsinA" semispecific="false"><rule index="1" sense="C-Term" cleave="FL" restrict="" /></protease><protease name="Tryp-CNBr" semispecific="false"><rule index="1" sense="C-Term" cleave="KMR" restrict="P" /></protease><protease name="TrypChymo" semispecific="false"><rule index="1" sense="C-Term" cleave="FKLRWY" restrict="P" /></protease><protease name="Trypsin/P" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="" /></protease><protease name="Trypsin/P+DP" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="ACDEFGHIJKLMNQRSTVWY" /></protease><protease name="V8-DE" semispecific="false"><rule index="1" sense="C-Term" cleave="DE" restrict="P" /></protease><protease name="V8-E" semispecific="false"><rule index="1" sense="C-Term" cleave="E" restrict="P" /></protease><protease name="semiTrypsin" semispecific="true"><rule index="1" sense="C-Term" cleave="KR" restrict="P" /></protease><protease name="LysC+AspN" semispecific="false"><rule index="1" sense="N-Term" cleave="D" restrict="" /><rule index="2" sense="C-Term" cleave="K" restrict="P" /></protease><protease name="Lys-C/P+DP" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="ACDEFGHIJKLMNQRSTVWY" /></protease><protease name="Trypsin/P + Asp-N" semispecific="false"><rule index="1" sense="N-Term" cleave="D" restrict="" /><rule index="2" sense="C-Term" cleave="KR" restrict="" /></protease><protease name="Asp-C" semispecific="false"><rule index="1" sense="C-Term" cleave="D" restrict="" /></protease><protease name="Trypsin/P+Asp-C" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="" /></protease><protease name="SemiLys" semispecific="true"><rule index="1" sense="C-Term" cleave="K" restrict="" /></protease><protease name="SemiGluC" semispecific="true"><rule index="1" sense="C-Term" cleave="DE" restrict="" /></protease><protease name="LysC/P+AspC" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="" /></protease><protease name="GluC" semispecific="false"><rule index="1" sense="C-Term" cleave="E" restrict="" /></protease></proteases>
\ No newline at end of file

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/BSA_min_23.mzXML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BSA_min_23.mzXML Sat Jul 20 05:01:05 2019 -0400

b'@@ -0,0 +1,2198 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"\n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n+ <msRun scanCount="100" startTime="PT0.1507S" endTime="PT35.6487S">\n+ <parentFile fileName="file:///D:\\shared\\dglaetzer\\maxquant_tool\\more rawfiles/BSA_min_23.raw"\n+ fileType="RAWData"\n+ fileSha1="63ee877fecd36e6af38642812ac2b877185f92af"/>\n+ <msInstrument msInstrumentID="1">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ Orbitrap XL"/>\n+ <msIonisation category="msIonisation" value="nanoelectrospray"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="orbitrap"/>\n+ <msDetector category="msDetector" value="inductive detector"/>\n+ <software type="acquisition" name="Xcalibur" version="2.5.5 SP2"/>\n+ </msInstrument>\n+ <msInstrument msInstrumentID="2">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ Orbitrap XL"/>\n+ <msIonisation category="msIonisation" value="nanoelectrospray"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="radial ejection linear ion trap"/>\n+ <msDetector category="msDetector" value="electron multiplier"/>\n+ <software type="acquisition" name="Xcalibur" version="2.5.5 SP2"/>\n+ </msInstrument>\n+ <dataProcessing centroided="1">\n+ <software type="conversion" name="ProteoWizard software" version="3.0.9706"/>\n+ <processingOperation name="Conversion to mzML"/>\n+ <software type="processing" name="ProteoWizard software" version="3.0.9706"/>\n+ <comment>Thermo/Xcalibur peak picking</comment>\n+ </dataProcessing>\n+ <scan num="1"\n+ scanType="Full"\n+ centroided="1"\n+ msLevel="1"\n+ peaksCount="782"\n+ polarity="+"\n+ retentionTime="PT0.1507S"\n+ lowMz="370.207244873047"\n+ highMz="1672.387329101563"\n+ basePeakMz="395.239288330078"\n+ basePeakIntensity="1.859395375e06"\n+ totIonCurrent="2.3434522e07"\n+ msInstrumentID="1">\n+ <peaks compressionType="zlib"\n+ compressedLen="5759"\n+ precision="32"\n+ byteOrder="network"\n+ 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</scan>\n+ </msRun>\n+ <index name="scan">\n+ <offset id="1">1921</offset>\n+ <offset id="2">10191</offset>\n+ <offset id="3">13306</offset>\n+ <offset id="4">18933</offset>\n+ <offset id="5">22172</offset>\n+ <offset id="6">25947</offset>\n+ <offset id="7">29042</offset>\n+ <offset id="8">38308</offset>\n+ <offset id="9">42036</offset>\n+ <offset id="10">46110</offset>\n+ <offset id="11">50049</offset>\n+ <offset id="12">52906</offset>\n+ <offset id="13">56010</offset>\n+ <offset id="14">65016</offset>\n+ <offset id="15">67927</offset>\n+ <offset id="16">71250</offset>\n+ <offset id="17">75804</offset>\n+ <offset id="18">79136</offset>\n+ <offset id="19">82202</offset>\n+ <offset id="20">90776</offset>\n+ <offset id="21">93593</offset>\n+ <offset id="22">97558</offset>\n+ <offset id="23">101451</offset>\n+ <offset id="24">104054</offset>\n+ <offset id="25">106797</offset>\n+ <offset id="26">115518</offset>\n+ <offset id="27">117804</offset>\n+ <offset id="28">120302</offset>\n+ 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diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/bsa.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.fasta Sat Jul 20 05:01:05 2019 -0400

@@ -0,0 +1,12 @@
+>bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4
+MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPF
+DEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEP
+ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYY
+ANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVA
+RLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE
+CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRR
+HPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEK
+LGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLIL
+NRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLP
+DTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV
+STQTALA

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/exp_design_test.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exp_design_test.txt Sat Jul 20 05:01:05 2019 -0400

@@ -0,0 +1,3 @@
+Name Fraction Experiment PTM
+QEplus021874 3 1
+QEplus021876 4 2

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/allPeptides.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/allPeptides.txt Sat Jul 20 05:01:05 2019 -0400

[

b'@@ -0,0 +1,166 @@\n+Raw file\tType\tCharge\tm/z\tMass\tUncalibrated m/z\tResolution\tNumber of data points\tNumber of scans\tNumber of isotopic peaks\tPIF\tMass fractional part\tMass deficit\tMass precision [ppm]\tMax intensity m/z 0\tRetention time\tRetention length\tRetention length (FWHM)\tMin scan number\tMax scan number\tIdentified\tMS/MS IDs\tSequence\tLength\tModifications\tModified sequence\tProteins\tScore\tIntensity\tIntensities\tIsotope pattern\tMS/MS Count\tMSMS Scan Numbers\tMSMS Isotope Indices\r\n+BSA_min_23\tMULTI\t3\t710.69967\t2129.0772\t710.69967\tNaN\t5\t3\t2\t\t0.077192\t0.0578164096173168\t1.180035\t711.033930698172\t0.037\t8.255\t0\t1\t25\t\t-1\t \t0\t \t \t \tNaN\t27555\t0;16823.720703125;10726.12109375;6644.5966796875;0\t7737.3974609375;9086.3232421875\t0\t\t\r\n+BSA_min_23\tMULTI\t3\t1567.4354\t4699.2845\t1567.4354\tNaN\t5\t3\t2\t\t0.284514\t0.0828426326752378\t7.986968\t1568.10387245715\t0.067\t8.255\t0\t1\t25\t\t-1\t \t0\t \t \t \tNaN\t137580\t0;23479.5932617188;59085.9194335938;20990.259765625;0\t0;0;53540.3203125;7305.36279296875\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t466.26817\t930.5218\t466.26817\tNaN\t6\t4\t2\t\t0.521797\t0.0537564853223103\t1.477127\t466.26850803291\t0.107\t10.33\t0\t1\t31\t\t-1\t \t0\t \t \t \tNaN\t33499\t0;16896.8359375;13251.4482421875;29638.681640625;21903.5859375;0\t22962.34375;6676.337890625\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t835.80692\t1669.5993\t835.80692\tNaN\t7\t4\t2\t\t0.599289\t-0.208726257088529\t1.196939\t835.807035746435\t0.107\t10.33\t0\t1\t31\t\t-1\t \t0\t \t \t \tNaN\t35250\t0;14611.8764648438;18125.6357421875;25099.0166015625;15365.583984375;0\t16483.943359375;8615.0732421875\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t889.42648\t1776.8384\t889.42648\tNaN\t6\t3\t2\t\t0.838398\t-0.0189472723534436\t2.943901\t889.927320499287\t0.107\t8.255\t0\t1\t25\t\t-1\t \t0\t \t \t \tNaN\t24592\t0;9125.99072265625;13286.1201171875;16742.716796875;0\t7208.8173828125;9533.8994140625\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t378.70717\t755.39978\t378.70717\tNaN\t4\t2\t2\t\t0.399783\t0.0122990350871532\t2.895866\t378.7066995797\t0.119\t6.221\t0\t13\t31\t\t-1\t \t0\t \t \t \tNaN\t17113\t0;15764.96875;12169.2568359375;0\t9865.826171875;5910.52587890625\t0\t\t\r\n+BSA_min_23\tMULTI\t6\t456.58136\t2733.4445\t456.58136\tNaN\t6\t5\t2\t\t0.444504\t0.14711979940148\t1.365307\t456.748107866223\t0.139\t12.618\t0\t7\t43\t\t-1\t \t0\t \t \t \tNaN\t36582\t0;9077.5439453125;13902.0874023438;19992.689453125;13010.4306640625;0;0\t0;13844.125;6148.564453125\t1\t8\t1\r\n+BSA_min_23\tMULTI\t2\t701.87367\t1401.7328\t701.87367\tNaN\t4\t2\t2\t\t0.732779\t0.0479819779827722\t2.085359\t701.87287295525\t0.139\t6.221\t0\t13\t31\t\t-1\t \t0\t \t \t \tNaN\t19640\t0;11736.2470703125;14934.2939453125;0\t8433.541015625;6500.7529296875\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t903.84665\t1805.6788\t903.84665\tNaN\t14\t5\t3\t\t0.67875\t-0.191861895242255\t0.587413\t903.846381489202\t0.128\t12.505\t0\t1\t37\t\t-1\t \t0\t \t \t \tNaN\t89876\t0;22660.5712890625;48080.4096679688;66770.5043945313;78759.361328125;39740.7744140625;0\t39216.41796875;30181.7421875;16944.533203125\t1\t27\t0\r\n+BSA_min_23\tMULTI\t3\t487.53462\t1459.582\t487.53462\tNaN\t16\t8\t3\t\t0.582041\t-0.129367074224319\t0.655422\t487.53461224021\t0.133\t19.043\t0\t1\t55\t\t-1\t \t0\t \t \t \tNaN\t84731\t0;7211.73095703125;32638.8959960938;79787.74609375;74581.1875;40743.359375;31912.87890625;10748.6064453125;5496.4296875;0\t40288.40234375;32200.93359375;13735.64453125\t1\t33\t1\r\n+BSA_min_23\tMULTI\t3\t583.22015\t1746.6386\t583.22015\tNaN\t7\t4\t2\t\t0.638625\t-0.204828530265331\t2.286815\t583.220239813966\t0.176\t10.457\t0\t7\t37\t\t-1\t \t0\t \t \t \tNaN\t42292\t0;4036.83081054688;17411.11328125;19834.8046875;29221.802734375;0\t17431.560546875;11790.2421875\t0\t\t\r\n+BSA_min_23\tMULTI\t3\t635.60251\t1903.7857\t635.60251\tNaN\t11\t5\t3\t\t0.785698\t-0.130043202729439\t1.119621\t635.602244079812\t0.167\t12.618\t0\t7\t43\t\t-1\t \t0\t \t \t \tNaN\t45493\t0;8725.0478515625;17613.3891601563;33308.2824707031;39386.6171875;0;0\t17209.375;13758.326171875;9491.1767578125\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t730.79903\t1459.5835\t730.79903\tNaN\t10\t6\t2\t\t0.583509\t-0.127899156014337\t0.609982\t730.799136547346\t0.151\t14.666\t0\t1\t43\t\t-1\t \t0\t \t \t \tNaN\t77496\t0;5839.765625;27434.9599609375;42471.279296875;58278.560546875;32345.4384765625;15650.7568359375;0\t39553.00390625;19513.171875\t1\t29\t0\r\n+BSA_min_23\tMULTI\t2\t996.94429\t1991.874\t996.94429\tNaN\t15\t13\t2\t\t0'..b'\t11\t4\t3\t\t0.571176\t-0.132406498940327\t0.529807\t722.794557009268\t0.587\t8.245\t0\t81\t99\t\t-1\t \t0\t \t \t \tNaN\t88555\t0;19382.1572265625;29263.3842773438;56304.751953125;72047.59765625;0\t31798.40625;40249.19140625;9051.69140625\t2\t94;97\t0;0\r\n+BSA_min_23\tMULTI\t2\t731.29826\t1460.582\t731.29826\tNaN\t9\t5\t2\t\t0.581963\t-0.129905034647663\t1.015729\t731.799523381077\t0.526\t10.085\t0\t75\t99\t\t-1\t \t0\t \t \t \tNaN\t29169\t0;10700.2763671875;21935.4814453125;17981.1000976563;13056.220703125;17802.30078125;0\t11073.208984375;11301.125\t1\t90\t0\r\n+BSA_min_23\tMULTI\t2\t772.32634\t1542.6381\t772.32634\tNaN\t16\t12\t3\t\t0.638121\t-0.111492432172099\t0.832583\t772.326445295162\t0.587\t24.286\t0\t37\t99\t\t-1\t \t0\t \t \t \tNaN\t48065\t0;8672.376953125;7721.82470703125;8208.14233398438;8694.4599609375;12981.9775390625;10428.1220703125;10370.2294921875;9308.8408203125;12825.458984375;17852.220703125;30189.3129882813;24380.708984375;0\t19063.345703125;15360.51953125;9020.189453125\t0\t\t\r\n+BSA_min_23\tMULTI\t3\t776.67069\t2326.9902\t776.67069\tNaN\t7\t3\t3\t\t0.990245\t-0.120170237694765\t2.142655\t777.004331643663\t0.571\t6.087\t0\t87\t99\t\t-1\t \t0\t \t \t \tNaN\t37194\t0;6977.5546875;29906.751953125;25277;0\t9063.5791015625;14645.7783203125;12678.326171875\t0\t\t\r\n+BSA_min_23\tMULTI\t1\t837.43637\t836.42909\t837.43637\tNaN\t7\t4\t2\t\t0.429093\t0.0043357496634826\t1.321128\t837.436103089852\t0.587\t8.245\t0\t81\t99\t\t-1\t \t0\t \t \t \tNaN\t73009\t0;8795.1123046875;28166.4892578125;33590.7690429688;65961.154296875;0\t53311.69140625;12649.462890625\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t882.84611\t1763.6777\t882.84611\tNaN\t12\t7\t3\t\t0.677665\t-0.17362702288824\t0.483171\t882.846072087715\t0.563\t13.784\t0\t65\t99\t\t-1\t \t0\t \t \t \tNaN\t1179300\t0;10685.890625;57645.44140625;185231.5625;292455.5625;750275.78125;1040647.75;871335.640625;0\t494015.65625;379948.71875;166683.375\t1\t100\t0\r\n+BSA_min_23\tMULTI\t2\t886.81224\t1771.6099\t886.81224\tNaN\t8\t5\t2\t\t0.609919\t-0.245021216350096\t1.522474\t887.31412154531\t0.576\t10.085\t0\t75\t99\t\t-1\t \t0\t \t \t \tNaN\t29012\t0;5249.1533203125;6298.3564453125;13226.2900390625;17856.4375;20045.5546875;0\t8890.65234375;11784.896484375\t0\t\t\r\n+BSA_min_23\tMULTI\t1\t899.44874\t898.44146\t899.44874\tNaN\t10\t6\t2\t\t0.441463\t-0.0118196933137824\t0.473138\t899.44868329937\t0.563\t11.938\t0\t71\t99\t\t-1\t \t0\t \t \t \tNaN\t93356\t0;10259.021484375;11104.9755859375;38988.1611328125;51494.2109375;83477.83203125;72926.943359375;0\t61125.3359375;22352.49609375\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t973.90466\t1945.7948\t973.90466\tNaN\t7\t4\t2\t\t0.794757\t-0.14030840214582\t1.357784\t973.904958275679\t0.587\t8.245\t0\t81\t99\t\t-1\t \t0\t \t \t \tNaN\t67032\t0;22343.408203125;30602.4375;39709.193359375;30783.283203125;0\t30783.283203125;12774.3359375\t0\t\t\r\n+BSA_min_23\tMULTI\t1\t1012.4647\t1011.4574\t1012.4647\tNaN\t10\t6\t2\t\t0.457396\t-0.0478741148867812\t0.66179\t1012.46465963589\t0.58\t11.938\t0\t71\t99\t\t-1\t \t0\t \t \t \tNaN\t45315\t0;6566.83447265625;5892.9794921875;22179.6865234375;26302.4379882813;35693.482421875;39795.4755859375;0\t31461.541015625;12683.193359375\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t1044.9323\t2087.8501\t1044.9323\tNaN\t6\t4\t2\t\t0.850137\t-0.150273671131799\t1.779455\t1045.43259299012\t0.587\t8.245\t0\t81\t99\t\t-1\t \t0\t \t \t \tNaN\t22292\t0;6181.01806640625;6017.2158203125;11961.13671875;13880.3842773438;0\t6740.865234375;7139.51904296875\t0\t\t\r\n+BSA_min_23\tMULTI\t2\t1074.9485\t2147.8825\t1074.9485\tNaN\t7\t5\t2\t\t0.882505\t-0.145520540587768\t1.74705\t1074.94713499826\t0.56\t10.085\t0\t75\t99\t\t-1\t \t0\t \t \t \tNaN\t47904\t0;7807.28466796875;5717.341796875;13474.2958984375;16493.6396484375;19157.744140625;0\t13474.2958984375;10645.7109375\t0\t\t\r\n+BSA_min_23\tMULTI\t1\t1164.5167\t1163.5094\t1164.5167\tNaN\t6\t4\t2\t\t0.50944\t-0.065774688654983\t0.883473\t1164.51651446826\t0.569\t8.245\t0\t81\t99\t\t-1\t \t0\t \t \t \tNaN\t30247\t0;5882.703125;19118.6171875;25656.2758789063;16791.0786132813;0\t19902.078125;6989.12060546875\t0\t\t\r\n+BSA_min_23\tMULTI\t1\t1177.4707\t1176.4634\t1177.4707\tNaN\t18\t7\t3\t\t0.463421\t-0.117752640125445\t0.401898\t1177.47052434449\t0.565\t13.784\t0\t65\t99\t\t-1\t \t0\t \t \t \tNaN\t191160\t0;13462.1650390625;32176.0517578125;66198.634765625;127578.37890625;153005.427734375;176360.41015625;148912.65625;0\t107823.8203125;52374.53515625;18917.345703125\t1\t64\t0\r\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/evidence.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/evidence.txt Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,7 @@
+Sequence Length Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs Oxidation (M) Missed cleavages Proteins Leading proteins Leading razor protein Type Raw file Experiment MS/MS m/z Charge m/z Mass Resolution Uncalibrated - Calibrated m/z [ppm] Uncalibrated - Calibrated m/z [Da] Mass error [ppm] Mass error [Da] Uncalibrated mass error [ppm] Uncalibrated mass error [Da] Max intensity m/z 0 Retention time Retention length Calibrated retention time Calibrated retention time start Calibrated retention time finish Retention time calibration Match time difference Match m/z difference Match q-value Match score Number of data points Number of scans Number of isotopic peaks PIF Fraction of total spectrum Base peak fraction PEP MS/MS count MS/MS scan number Score Delta score Combinatorics Intensity Reverse Potential contaminant id Protein group IDs Peptide ID Mod. peptide ID MS/MS IDs Best MS/MS AIF MS/MS IDs Oxidation (M) site IDs
+DSFDIIK 7 Unmodified _DSFDIIK_ 0 0 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 419.221313476563 2 419.221268 836.427984 NaN 0 0 0.54276 0.00022754 0.54276 0.00022754 419.22139467134 0.58669 0.13742 0.58669 0.46121 0.59862 0 11 4 3 0 0 0 0.010549 1 96 0 0 1 768320 + 0 2 0 0 0 0
+LLESEECR 8 Unmodified _LLESEECR_ 0 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 CON__Q14CN4-1 MSMS BSA_min_23 BSA_min_23.mzXML 518.238220214844 2 518.242406 1034.47026 NaN NaN NaN NaN NaN NaN NaN NaN 0.50957 1 0.50957 0.0095717 1.0096 0 0 0 0 0.0075205 1 86 1.6313 1.6313 1 + 1 5 1 1 1 1
+LVTDLTK 7 Unmodified _LVTDLTK_ 0 0 CON__P02769;bsa;CON__P02768-1 CON__P02769 CON__P02769 MSMS BSA_min_23 BSA_min_23.mzXML 395.239288330078 2 395.239461 788.46437 NaN NaN NaN NaN NaN NaN NaN NaN 0.010013 1 0.010013 -0.48999 0.51001 0 0 0 0 0.0046553 1 2 0 0 1 + 2 0 2 2 2 2
+QLELEKQLEK 10 Unmodified _QLELEKQLEK_ 0 1 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 419.221313476563 3 419.906482 1256.69762 NaN 0 0 0.052788 2.2166E-05 0.052788 2.2166E-05 419.9067499241 0.32847 0.47559 0.32847 0.12303 0.59862 0 25 14 2 0 0 0 0.011549 1 96 0 0 1 57554 + 3 1 3 3 3 3
+SLSAIRER 8 Unmodified _SLSAIRER_ 0 1 CON__Q03247 CON__Q03247 CON__Q03247 MULTI-SECPEP BSA_min_23 BSA_min_23.mzXML 465.766693115234 2 466.269616 930.524678 NaN 0 0 -3.0904 -0.0014409 -3.0904 -0.0014409 466.26850803291 0.10674 0.17216 0.10674 -0.014552 0.15761 0 6 4 2 0 0 0 0.011549 1 17 0 0 1 33499 + 4 4 4 4 4 4
+TLGPWGQR 8 Unmodified _TLGPWGQR_ 0 0 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 MULTI-MSMS BSA_min_23 BSA_min_23.mzXML 457.746032714844 2 457.745776 913.477 NaN 0 0 -0.28456 -0.00013026 -0.28456 -0.00013026 457.745456355006 0.4547 0.40477 0.4547 0.19386 0.59862 -5.5511E-17 18 12 2 0 0 0 0.01108 1 72 0 0 1 61894 + 5 3 5 5 5 5

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/modificationSpecificPeptides.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/modificationSpecificPeptides.txt Sat Jul 20 05:01:05 2019 -0400

@@ -0,0 +1,7 @@
+Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Unique (Groups) Unique (Proteins) Oxidation (M) Missed cleavages Experiment BSA_min_23.mzXML Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Intensity Intensity BSA_min_23.mzXML Reverse Potential contaminant id Protein group IDs Peptide ID Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count
+DSFDIIK Unmodified 836.42798 0.42798405 2 CON__ENSEMBL:ENSBTAP00000016046 yes yes 0 0 1 0.58669 0.58669 2 0.010549 96 BSA_min_23 0 0 768320 768320 + 0 2 0 0 0 0 1
+LLESEECR Unmodified 1034.4703 0.47025958 5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 yes no 0 0 1 0.50957 0.50957 2 0.0075205 86 BSA_min_23 1.6313 1.6313 0 0 + 1 5 1 1 1 1 1
+LVTDLTK Unmodified 788.46437 0.46436956 0 CON__P02769;bsa;CON__P02768-1 yes no 0 0 1 0.010013 0.010013 2 0.0046553 2 BSA_min_23 0 0 0 0 + 2 0 2 2 2 2 1
+QLELEKQLEK Unmodified 1256.6976 0.69761697 1 CON__ENSEMBL:ENSBTAP00000001528 yes yes 0 1 1 0.32847 0.32847 3 0.011549 96 BSA_min_23 0 0 57554 57554 + 3 1 3 3 3 3 0
+SLSAIRER Unmodified 930.52468 0.52467841 4 CON__Q03247 yes yes 0 1 1 0.10674 0.10674 2 0.011549 17 BSA_min_23 0 0 33499 33499 + 4 4 4 4 4 4 0
+TLGPWGQR Unmodified 913.477 0.47699993 3 CON__ENSEMBL:ENSBTAP00000018574 yes yes 0 0 1 0.4547 0.4547 2 0.01108 72 BSA_min_23 0 0 61894 61894 + 5 3 5 5 5 5 1

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/msms.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/msms.txt Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,7 @@
+Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score Diffs Oxidation (M) Proteins Charge Fragmentation Mass analyzer Type Scan event number Isotope index m/z Mass Mass error [ppm] Mass error [Da] Simple mass error [ppm] Retention time PEP Score Delta score Score diff Localization prob Combinatorics PIF Fraction of total spectrum Base peak fraction Precursor Full ScanNumber Precursor Intensity Precursor Apex Fraction Precursor Apex Offset Precursor Apex Offset Time Matches Intensities Mass Deviations [Da] Mass Deviations [ppm] Masses Number of Matches Intensity coverage Peak coverage Neutral loss level ETD identification type Reverse All scores All sequences All modified sequences id Protein group IDs Peptide ID Mod. peptide ID Evidence ID Oxidation (M) site IDs
+BSA_min_23 96 77 DSFDIIK 7 0 Unmodified _DSFDIIK_ 0 CON__ENSEMBL:ENSBTAP00000016046 2 CID FTMS MULTI-MSMS 1 0 419.22127 836.42798 0.54276 0.00022754 NaN 0.57043 0.010549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 DSFDIIK _DSFDIIK_ 0 2 0 0 0
+BSA_min_23 86 70 LLESEECR 8 0 Unmodified _LLESEECR_ 0 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 2 CID FTMS MSMS 5 518.24241 1034.4703 NaN NaN NaN 0.50957 0.0075205 1.6313 1.6313 NaN NaN 1 0 0 0 81 10271.2001953125 1 0 0 y6 11.7 0.0135096433999706 16.6930827476743 809.2958984375 1 0.00309955136349784 0.00847457627118644 None Unknown 1.63126590808724;0;0 LLESEECR;LGSDMEDLR;QLNQEMEK _LLESEECR_;_LGSDMEDLR_;_QLNQEM(ox)EK_ 1 5 1 1 1
+BSA_min_23 2 0 LVTDLTK 7 0 Unmodified _LVTDLTK_ 0 CON__P02769;bsa;CON__P02768-1 2 CID FTMS MSMS 1 395.23946 788.46437 NaN NaN NaN 0.010013 0.0046553 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0;0 LVTDLTK;DSLLTLK _LVTDLTK_;_DSLLTLK_ 2 0 2 2 2
+BSA_min_23 96 77 QLELEKQLEK 10 1 Unmodified _QLELEKQLEK_ 0 CON__ENSEMBL:ENSBTAP00000001528 3 CID FTMS MULTI-SECPEP 1 -2 419.90648 1256.6976 0.052788 2.2166E-05 NaN 0.57043 0.011549 0 0 NaN NaN 1 0 0 0 95 346270.625 0.704625040984097 -1 0.0243583333333334 0 0 0 None Unknown 0 QLELEKQLEK _QLELEKQLEK_ 3 1 3 3 3
+BSA_min_23 17 13 SLSAIRER 8 1 Unmodified _SLSAIRER_ 0 CON__Q03247 2 CID FTMS MULTI-SECPEP 4 -1 466.26962 930.52468 -3.0904 -0.0014409 NaN 0.096553 0.011549 0 0 NaN NaN 1 0 0 0 -1 NaN NaN 0 NaN 0 0 0 None Unknown 0 SLSAIRER _SLSAIRER_ 4 4 4 4 4
+BSA_min_23 72 58 TLGPWGQR 8 0 Unmodified _TLGPWGQR_ 0 CON__ENSEMBL:ENSBTAP00000018574 2 CID FTMS MULTI-MSMS 1 0 457.74578 913.477 -0.28456 -0.00013026 NaN 0.42593 0.01108 0 0 NaN NaN 1 0 0 0 71 32936.3203125 0.758644306612328 -2 0.0615566666666666 0 0 0 None Unknown 0;0 TLGPWGQR;IHVFNER _TLGPWGQR_;_IHVFNER_ 5 3 5 5 5

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/msmsScans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/msmsScans.txt Sat Jul 20 05:01:05 2019 -0400

b'@@ -0,0 +1,82 @@\n+Raw file\tScan number\tRetention time\tIon injection time\tTotal ion current\tCollision energy\tSummations\tBase peak intensity\tElapsed time\tIdentified\tMS/MS IDs\tSequence\tLength\tFiltered peaks\tm/z\tMass\tCharge\tType\tFragmentation\tMass analyzer\tParent intensity fraction\tFraction of total spectrum\tBase peak fraction\tPrecursor full scan number\tPrecursor intensity\tPrecursor apex fraction\tPrecursor apex offset\tPrecursor apex offset time\tScan event number\tModifications\tModified sequence\tProteins\tScore\tExperiment\tIntens Comp Factor\tCTCD Comp\tRawOvFtT\tAGC Fill\tScan index\tMS scan index\tMS scan number\r\n+BSA_min_23\t2\t0.010013\t-1\t35863\t35\t0\t0\t-1\t+\t2\tLVTDLTK\t7\t103\t395.239288330078\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\tUnmodified\t_LVTDLTK_\tbsa;CON__P02768-1;CON__P02769\t0\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t0\t0\t1\r\n+BSA_min_23\t3\t0.01458\t-1\t30585\t35\t0\t0\t-1\t-\t-1\t \t0\t164\t552.918823242188\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t1\t0\t1\r\n+BSA_min_23\t4\t0.020265\t-1\t11886\t35\t0\t0\t-1\t-\t-1\t \t0\t126\t676.387463660038\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t2\t0\t1\r\n+BSA_min_23\t5\t0.025633\t-1\t12813\t35\t0\t0\t-1\t-\t-1\t \t0\t146\t751.810668945313\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t3\t0\t1\r\n+BSA_min_23\t6\t0.031253\t-1\t10791\t35\t0\t0\t-1\t-\t-1\t \t0\t124\t670.800842285156\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t4\t0\t1\r\n+BSA_min_23\t8\t0.044372\t-1\t7950.3\t35\t0\t0\t-1\t-\t-1\t \t0\t111\t456.581360511828\t2733.44450427137\t6\tMULTI\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t5\t1\t7\r\n+BSA_min_23\t9\t0.049315\t-1\t13730\t35\t0\t0\t-1\t-\t-1\t \t0\t120\t562.257629394531\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t6\t1\t7\r\n+BSA_min_23\t10\t0.05446\t-1\t8774.7\t35\t0\t0\t-1\t-\t-1\t \t0\t121\t589.203410887949\t588.196134421349\t1\tMULTI\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t7\t1\t7\r\n+BSA_min_23\t11\t0.06018\t-1\t4436.2\t35\t0\t0\t-1\t-\t-1\t \t0\t115\t828.876770019531\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t8\t1\t7\r\n+BSA_min_23\t12\t0.065908\t-1\t3625.8\t35\t0\t0\t-1\t-\t-1\t \t0\t112\t639.798400878906\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t9\t1\t7\r\n+BSA_min_23\t14\t0.078957\t-1\t13236\t35\t0\t0\t-1\t-\t-1\t \t0\t137\t883.333059829652\t1764.6515667261\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t13\t171569.53125\t0.0583552615411773\t-4\tNaN\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t10\t2\t13\r\n+BSA_min_23\t15\t0.084805\t-1\t6304.6\t35\t0\t0\t-1\t-\t-1\t \t0\t120\t602.8994140625\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t11\t2\t13\r\n+BSA_min_23\t16\t0.090573\t-1\t12119\t35\t0\t0\t-1\t-\t-1\t \t0\t135\t648.602708784548\t1942.78629695384\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t13\t52074.7734375\t0.102435594507697\t-16\tNaN\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t12\t2\t13\r\n+BSA_min_23\t17\t0.096553\t-1\t5932.3\t35\t0\t0\t-1\t-\t-1\t \t0\t110\t465.766693115234\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t4\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t13\t2\t13\r\n+BSA_min_23\t18\t0.10154\t-1\t4161.5\t35\t0\t0\t-1\t-\t-1\t \t0\t108\t605.758117675781\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t-1\tNaN\tNaN\t0\tNaN\t5\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t14\t2\t13\r\n+BSA_min_23\t20\t0.11439\t-1\t65173\t35\t0\t0\t-1\t-\t-1\t \t0\t102\t387.700285234344\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t19\t5176.81640625\t0.231645826498235\t-7\tNaN\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t15\t3\t19\r\n+BSA_min_23\t21\t0.11842\t-1\t33705\t35\t0\t0\t-1\t-\t-1\t \t0\t123\t430.226482307928\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t19\t7040.359375\t0.343536017509867\t-2\t0.0701033333333334\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t16\t3\t19\r\n+BSA_min_23\t22\t0.1234\t-1\t9502.6\t35\t0\t0\t-1\t-\t-1\t \t0\t111\t455.744353147131\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t19\t112493.5\t0.827447086298523\t-1\t0.0355433333333333\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t17\t3\t19\r\n+BSA_min_23\t23\t0.12833\t-1\t2553.5\t35\t0\t0\t-1\t-\t-1\t \t0\t105\t664.964606092136\t1991.87198887661\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t19\t58531.14453125\t1\t0\t0\t4\t \t \t'..b'zXML\tNaN\tNaN\tNaN\t0\t62\t13\t75\r\n+BSA_min_23\t78\t0.46188\t-1\t2747.5\t35\t0\t0\t-1\t-\t-1\t \t0\t106\t664.964606092136\t1991.87198887661\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t75\t18094.236328125\t0.676187560804335\t3\t-0.0957016666666666\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t63\t13\t75\r\n+BSA_min_23\t79\t0.46792\t-1\t3792.1\t35\t0\t0\t-1\t-\t-1\t \t0\t127\t782.86823361998\t1563.72191430676\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t75\t24751.693359375\t0.989113548898297\t-1\t0.0244116666666667\t4\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t64\t13\t75\r\n+BSA_min_23\t80\t0.4736\t-1\t1227.2\t35\t0\t0\t-1\t-\t-1\t \t0\t96\t1173.07641144645\t2344.1382699597\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t75\t23081.546875\t1\t0\t0\t5\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t65\t13\t75\r\n+BSA_min_23\t82\t0.48722\t-1\t6556.1\t35\t0\t0\t-1\t-\t-1\t \t0\t116\t629.356568937177\t1256.69858494115\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t28788.931640625\t1\t0\t0\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t66\t14\t81\r\n+BSA_min_23\t83\t0.4925\t-1\t6615.3\t35\t0\t0\t-1\t-\t-1\t \t0\t116\t559.768784063361\t1117.52301519352\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t35334.84765625\t0.949368528711517\t-1\t0.0369099999999999\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t67\t14\t81\r\n+BSA_min_23\t84\t0.49762\t-1\t6183.7\t35\t0\t0\t-1\t-\t-1\t \t0\t125\t972.401410273474\t1942.78826761375\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t19756.91796875\t0.347354270628424\t7\tNaN\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t68\t14\t81\r\n+BSA_min_23\t85\t0.50353\t-1\t3559.8\t35\t0\t0\t-1\t-\t-1\t \t0\t116\t681.999313403946\t2042.97611081204\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t81\t11550.4775390625\t0.629091502669348\t2\t-0.0587916666666667\t4\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t69\t14\t81\r\n+BSA_min_23\t86\t0.50957\t-1\t5114.2\t35\t0\t0\t-1\t+\t1\tLLESEECR\t8\t118\t518.240989833781\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t81\t10271.2001953125\t1\t0\t0\t5\tUnmodified\t_LLESEECR_\tCON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5\t1.63126590808724\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t70\t14\t81\r\n+BSA_min_23\t88\t0.52259\t-1\t44411\t35\t0\t0\t-1\t-\t-1\t \t0\t134\t385.207382835291\t384.200106368691\t1\tMULTI\tCID\tFTMS\t0\t0\t0\t87\t5929296.5\t0.739051055541228\t-3\t0.0963616666666667\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t71\t15\t87\r\n+BSA_min_23\t89\t0.52681\t-1\t3749.8\t35\t0\t0\t-1\t-\t-1\t \t0\t100\t597.066144900786\t2980.29434217093\t5\tMULTI\tCID\tFTMS\t0\t0\t0\t87\t19359.11328125\t0.820197080002651\t2\t-0.04811\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t72\t15\t87\r\n+BSA_min_23\t90\t0.53279\t-1\t3364.5\t35\t0\t0\t-1\t-\t-1\t \t0\t128\t731.29825780069\t1460.58196266818\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t87\t10634.3564453125\t0.960368079417471\t-1\t0.0350400000000001\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t73\t15\t87\r\n+BSA_min_23\t92\t0.54611\t-1\t4680.5\t35\t0\t0\t-1\t-\t-1\t \t0\t116\t582.760858227368\t1163.50716352154\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t46220.83984375\t0.762103661377976\t-2\t0.0587916666666667\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t74\t16\t91\r\n+BSA_min_23\t93\t0.55132\t-1\t3773.2\t35\t0\t0\t-1\t-\t-1\t \t0\t106\t635.60201346581\t1903.78421099763\t3\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t24284.580078125\t0.586968526901584\t-2\t0.0587916666666667\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t75\t16\t91\r\n+BSA_min_23\t94\t0.55721\t-1\t4670.5\t35\t0\t0\t-1\t-\t-1\t \t0\t143\t722.292864587666\t1442.57117624213\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t91\t14970.0166015625\t0.470778833500893\t-2\t0.0587916666666667\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t76\t16\t91\r\n+BSA_min_23\t96\t0.57043\t-1\t15235\t35\t0\t0\t-1\t+\t0\tDSFDIIK\t7\t110\t419.22149602984\t836.428439126479\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t95\t346270.625\t0.704625040984097\t-1\t0.0243583333333334\t1\tUnmodified\t_DSFDIIK_\tCON__ENSEMBL:ENSBTAP00000016046\t0\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t77\t17\t95\r\n+BSA_min_23\t97\t0.57533\t-1\t4806.4\t35\t0\t0\t-1\t-\t-1\t \t0\t129\t722.292864587666\t1442.57117624213\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t95\t26752.708984375\t0.841322322069994\t-1\t0.0243583333333334\t2\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t78\t17\t95\r\n+BSA_min_23\t98\t0.58084\t-1\t3667\t35\t0\t0\t-1\t-\t-1\t \t0\t113\t595.224647156549\tNaN\t0\tPEAK\tCID\tFTMS\t0\t0\t0\t95\t6964.16259765625\t0.341923515563021\t-1\t0.0243583333333334\t3\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t79\t17\t95\r\n+BSA_min_23\t100\t0.59414\t-1\t44171\t35\t0\t0\t-1\t-\t-1\t \t0\t176\t882.846108818038\t1763.67766470288\t2\tMULTI\tCID\tFTMS\t0\t0\t0\t99\t379571.375\t0.768338756470332\t1\tNaN\t1\t \t \t \tNaN\tBSA_min_23.mzXML\tNaN\tNaN\tNaN\t0\t80\t18\t99\r\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/mzRange.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/mzRange.txt Sat Jul 20 05:01:05 2019 -0400

[

b'@@ -0,0 +1,1881 @@\n+Raw file\tm/z\tPeaks / Da\tSingle peaks / Da\tIsotope patterns / Da\tSingle isotope patterns / Da\tSILAC pairs / Da\tIdentified SILAC pairs / Da\tSILAC identification rate [%]\tMS/MS / Da\tIdentified MS/MS / Da\tIdentification rate 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diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/mzTab.mzTab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/mzTab.mzTab Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,45 @@
+MTD mzTab-version 1.0.0
+MTD mzTab-mode Complete
+MTD mzTab-type Identification
+MTD title null
+MTD description null
+MTD software[1] [MS, MS:1001583, MaxQuant,1.6.3.4]
+COM [, CHEMMOD:57.0214637236, Carbamidomethyl (C),]
+MTD fixed_mod[1] [, , CHEMMOD:57.0214637236,]
+MTD fixed_mod[1]-site C
+MTD fixed_mod[1]-position Anywhere
+COM [, CHEMMOD:15.9949146221, Oxidation (M),]
+MTD variable_mod[1] [, , CHEMMOD:15.9949146221,]
+MTD variable_mod[1]-site M
+MTD variable_mod[1]-position Anywhere
+MTD protein_search_engine_score[1] [MS, MS:1002375, protein group-level combined FDRscore, ]
+MTD peptide_search_engine_score[1] [MS, MS:1001250, local FDR, ]
+MTD psm_search_engine_score[1] [MS, MS:1002338, Andromeda:score, ]
+MTD psm_search_engine_score[2] [MS, MS:1002995, Andromeda:PEP, ]
+MTD ms_run[1]-format [MS, MS:1002996, Andromeda:apl file format, ]
+MTD ms_run[1]-location file://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.secpep.sil0_0.apl
+MTD ms_run[1]-id_format [MS, MS:1000776, scan number only nativeID format, ]
+MTD ms_run[2]-format [MS, MS:1002996, Andromeda:apl file format, ]
+MTD ms_run[2]-location file://d:/shared/dglaetzer/maxquant_tool/test1/combined/andromeda/allspectra.cid.ftms.iso_0.apl
+MTD ms_run[2]-id_format [MS, MS:1000776, scan number only nativeID format, ]
+
+PRH accession description taxid species database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[1] search_engine_score[1]_ms_run[2] num_psms_ms_run[1] num_psms_ms_run[2] num_peptides_distinct_ms_run[1] num_peptides_distinct_ms_run[2] num_peptides_unique_ms_run[1] num_peptides_unique_ms_run[2] ambiguity_members modifications protein_coverage opt_global_cv_MS:1002217_decoy_peptide
+PRT CON__P02769 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 6.33205607832812 null null null null null null null null CON__P02769, bsa, CON__P02768-1 null 0.012 0
+PRT CON__ENSEMBL:ENSBTAP00000001528 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.93746772688895 null null null null null null null null CON__ENSEMBL:ENSBTAP00000001528 null 0.008 0
+PRT CON__ENSEMBL:ENSBTAP00000016046 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.97677849538172 null null null null null null null null CON__ENSEMBL:ENSBTAP00000016046 null 0.01 0
+PRT CON__ENSEMBL:ENSBTAP00000018574 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.95544937626172 null null null null null null null null CON__ENSEMBL:ENSBTAP00000018574 null 0.016 0
+PRT CON__Q03247 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 5.93746772688895 null null null null null null null null CON__Q03247 null 0.025 0
+PRT CON__Q14CN4-1 null null null null null [MS, MS:1002337, Andromeda, 1.6.3.4] 6.1237531147968 null null null null null null null null CON__Q14CN4-1, CON__Q3SY84, CON__Q9R0H5 null 0.016 0
+
+PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] search_engine_score[2] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_global_cv_MS:1000776_scan_number_only_nativeID_format opt_global_cv_MS:1002217_decoy_peptide
+PSM DSFDIIK 1 CON__ENSEMBL:ENSBTAP00000016046 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.010549248059121 null 0.570428333333333 2 419.22 419.22127 ms_run[2]:index=5 R R 646 652 96 0
+PSM LLESEECR 2 CON__Q14CN4-1 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 1.63126590808724 0.00752050293704335 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0
+PSM LLESEECR 2 CON__Q3SY84 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 1.63126590808724 0.00752050293704335 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0
+PSM LLESEECR 2 CON__Q9R0H5 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 1.63126590808724 0.00752050293704335 null 0.509571666666667 2 518.24 518.24241 ms_run[2]:index=13 K M 430 437 86 0
+PSM LVTDLTK 3 CON__P02769 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00465525978542915 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0
+PSM LVTDLTK 3 bsa 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00465525978542915 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0
+PSM LVTDLTK 3 CON__P02768-1 0 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.00465525978542915 null 0.0100133333333333 2 395.24 395.23946 ms_run[2]:index=4 K V 257 263 2 0
+PSM QLELEKQLEK 4 CON__ENSEMBL:ENSBTAP00000001528 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0115486780155693 null 0.570428333333333 3 419.91 419.90648 ms_run[1]:index=5 R Q 408 417 96 0
+PSM SLSAIRER 5 CON__Q03247 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0115486780155693 null 0.0965533333333333 2 466.27 466.26962 ms_run[1]:index=2 R F 190 197 17 0
+PSM TLGPWGQR 6 CON__ENSEMBL:ENSBTAP00000018574 1 null null [MS, MS:1002338, Andromeda:score, 1.6.3.4] 0 0.0110802771561295 null 0.425933333333333 2 457.75 457.74578 ms_run[2]:index=9 R D 20 27 72 0
+

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/parameters.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/parameters.txt Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,105 @@
+Parameter Value
+Version 1.6.3.4
+User name dglaetzer
+Machine name FPROT-BEAST
+Date of writing 04/04/2019 17:32:37
+Include contaminants True
+PSM FDR 0.01
+PSM FDR Crosslink 0.01
+Protein FDR 0.01
+Site FDR 0.01
+Use Normalized Ratios For Occupancy True
+Min. peptide Length 7
+Min. score for unmodified peptides 0
+Min. score for modified peptides 40
+Min. delta score for unmodified peptides 0
+Min. delta score for modified peptides 6
+Min. unique peptides 0
+Min. razor peptides 1
+Min. peptides 1
+Use only unmodified peptides and True
+Modifications included in protein quantification Oxidation (M)
+Peptides used for protein quantification Razor
+Discard unmodified counterpart peptides True
+Label min. ratio count 2
+Use delta score False
+iBAQ False
+iBAQ log fit False
+Match between runs False
+Find dependent peptides False
+Fasta file D:\fasta\bsa.fasta
+Decoy mode revert
+Include contaminants True
+Advanced ratios True
+Fixed andromeda index folder
+Temporary folder
+Combined folder location
+Second peptides True
+Stabilize large LFQ ratios True
+Separate LFQ in parameter groups False
+Require MS/MS for LFQ comparisons True
+Calculate peak properties False
+Main search max. combinations 200
+Advanced site intensities True
+Write msScans table False
+Write msmsScans table True
+Write ms3Scans table True
+Write allPeptides table True
+Write mzRange table True
+Write pasefMsmsScans table True
+Write accumulatedPasefMsmsScans table True
+Max. peptide mass [Da] 4600
+Min. peptide length for unspecific search 8
+Max. peptide length for unspecific search 25
+Razor protein FDR True
+Disable MD5 False
+Max mods in site table 3
+Match unidentified features False
+Epsilon score for mutations
+Evaluate variant peptides separately True
+Variation mode None
+MS/MS tol. (FTMS) 20 ppm
+Top MS/MS peaks per Da interval. (FTMS) 12
+Da interval. (FTMS) 100
+MS/MS deisotoping (FTMS) True
+MS/MS deisotoping tolerance (FTMS) 7
+MS/MS deisotoping tolerance unit (FTMS) ppm
+MS/MS higher charges (FTMS) True
+MS/MS water loss (FTMS) True
+MS/MS ammonia loss (FTMS) True
+MS/MS dependent losses (FTMS) True
+MS/MS recalibration (FTMS) False
+MS/MS tol. (ITMS) 0.5 Da
+Top MS/MS peaks per Da interval. (ITMS) 8
+Da interval. (ITMS) 100
+MS/MS deisotoping (ITMS) False
+MS/MS deisotoping tolerance (ITMS) 0.15
+MS/MS deisotoping tolerance unit (ITMS) Da
+MS/MS higher charges (ITMS) True
+MS/MS water loss (ITMS) True
+MS/MS ammonia loss (ITMS) True
+MS/MS dependent losses (ITMS) True
+MS/MS recalibration (ITMS) False
+MS/MS tol. (TOF) 40 ppm
+Top MS/MS peaks per Da interval. (TOF) 10
+Da interval. (TOF) 100
+MS/MS deisotoping (TOF) True
+MS/MS deisotoping tolerance (TOF) 0.01
+MS/MS deisotoping tolerance unit (TOF) Da
+MS/MS higher charges (TOF) True
+MS/MS water loss (TOF) True
+MS/MS ammonia loss (TOF) True
+MS/MS dependent losses (TOF) True
+MS/MS recalibration (TOF) False
+MS/MS tol. (Unknown) 0.5 Da
+Top MS/MS peaks per Da interval. (Unknown) 8
+Da interval. (Unknown) 100
+MS/MS deisotoping (Unknown) False
+MS/MS deisotoping tolerance (Unknown) 0.15
+MS/MS deisotoping tolerance unit (Unknown) Da
+MS/MS higher charges (Unknown) True
+MS/MS water loss (Unknown) True
+MS/MS ammonia loss (Unknown) True
+MS/MS dependent losses (Unknown) True
+MS/MS recalibration (Unknown) False
+Site tables Oxidation (M)Sites.txt

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/peptideSection.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/peptideSection.txt Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,7 @@
+PEH sequence accession unique database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[0] modifications retention_time retention_time_window charge mass_to_charge spectra_ref peptide_abundance_study_variable[0] peptide_abundance_stdev_study_variable[0] peptide_abundance_std_error_study_variable[0]
+PEP DSFDIIK null
+PEP LLESEECR null
+PEP LVTDLTK null
+PEP QLELEKQLEK null
+PEP SLSAIRER null
+PEP TLGPWGQR null

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/peptides.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/peptides.txt Sat Jul 20 05:01:05 2019 -0400

@@ -0,0 +1,7 @@
+Sequence N-term cleavage window C-term cleavage window Amino acid before First amino acid Second amino acid Second last amino acid Last amino acid Amino acid after A Count R Count N Count D Count C Count Q Count E Count G Count H Count I Count L Count K Count M Count F Count P Count S Count T Count W Count Y Count V Count U Count O Count Length Missed cleavages Mass Proteins Leading razor protein Start position End position Unique (Groups) Unique (Proteins) Charges PEP Score Experiment BSA_min_23.mzXML Intensity Intensity BSA_min_23.mzXML Reverse Potential contaminant id Protein group IDs Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count
+DSFDIIK NHADIIFDITDGNLRDSFDIIKRYMDGMTV DITDGNLRDSFDIIKRYMDGMTVGVVRQVR R D S I K R 0 0 0 2 0 0 0 0 0 2 0 1 0 1 0 1 0 0 0 0 0 0 7 0 836.42798 CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 646 652 yes yes 2 0.010549 0 1 768320 768320 + 0 2 0 0 0 0 1
+LLESEECR SLKLALDMEIATYRKLLESEECRMSGEYPN EIATYRKLLESEECRMSGEYPNSVSISVIS K L L C R M 0 1 0 0 1 0 3 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 8 0 1034.4703 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1 430 437 yes no 2 0.0075205 1.6313 1 0 0 + 1 5 1 1 1 1 1
+LVTDLTK LSQKFPKAEFVEVTKLVTDLTKVHKECCHG AEFVEVTKLVTDLTKVHKECCHGDLLECAD K L V T K V 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 0 2 0 0 1 0 0 7 0 788.46437 CON__P02769;bsa;CON__P02768-1 CON__P02769 257 263 yes no 2 0.0046553 0 1 0 0 + 2 0 2 2 2 2 1
+QLELEKQLEK QERKERERQEQERKRQLELEKQLEKQRELE QERKRQLELEKQLEKQRELERQREEERRKE R Q L E K Q 0 0 0 0 0 2 3 0 0 0 3 2 0 0 0 0 0 0 0 0 0 0 10 1 1256.6976 CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 408 417 yes yes 3 0.011549 0 1 57554 57554 + 3 1 3 3 3 3 0
+SLSAIRER RLAVYQAGASEGAERSLSAIRERFGPLVEQ ASEGAERSLSAIRERFGPLVEQGQSRAATL R S L E R F 1 2 0 0 0 0 1 0 0 1 1 0 0 0 0 2 0 0 0 0 0 0 8 1 930.52468 CON__Q03247 CON__Q03247 190 197 yes yes 2 0.011549 0 1 33499 33499 + 4 4 4 4 4 4 0
+TLGPWGQR LRPLLLALLLASACRTLGPWGQRDDGGGEP LLASACRTLGPWGQRDDGGGEPESMEPRWG R T L Q R D 0 1 0 0 0 1 0 2 0 0 1 0 0 0 1 0 1 1 0 0 0 0 8 0 913.477 CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 20 27 yes yes 2 0.01108 0 1 61894 61894 + 5 3 5 5 5 5 1

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/proteinGroups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/proteinGroups.txt Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,7 @@
+Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Peptides BSA_min_23.mzXML Razor + unique peptides BSA_min_23.mzXML Unique peptides BSA_min_23.mzXML Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Sequence coverage BSA_min_23.mzXML [%] Intensity Intensity BSA_min_23.mzXML MS/MS count Only identified by site Reverse Potential contaminant id Peptide IDs Peptide is razor Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Oxidation (M) site positions
+CON__P02769;bsa;CON__P02768-1 CON__P02769;bsa;CON__P02768-1 1;1;1 1;1;1 1;1;1 ;bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4; 3 1 1 1 1 1 1 1.2 1.2 1.2 69.293 607 607;607;609 0 6.3321 1.2 0 0 1 + 0 2 True 2 2 2 2
+CON__ENSEMBL:ENSBTAP00000001528 CON__ENSEMBL:ENSBTAP00000001528 1 1 1 1 1 1 1 1 1 1 0.8 0.8 0.8 137.98 1222 1222 0 5.9375 0.8 57554 57554 0 + 1 3 True 3 3 3 3
+CON__ENSEMBL:ENSBTAP00000016046 CON__ENSEMBL:ENSBTAP00000016046 1 1 1 1 1 1 1 1 1 1 1 1 1 77.456 706 706 0 5.9768 1 768320 768320 1 + 2 0 True 0 0 0 0
+CON__ENSEMBL:ENSBTAP00000018574 CON__ENSEMBL:ENSBTAP00000018574 1 1 1 1 1 1 1 1 1 1 1.6 1.6 1.6 55.207 496 496 0 5.9554 1.6 61894 61894 1 + 3 5 True 5 5 5 5
+CON__Q03247 CON__Q03247 1 1 1 1 1 1 1 1 1 1 2.5 2.5 2.5 35.979 316 316 0 5.9375 2.5 33499 33499 0 + 4 4 True 4 4 4 4
+CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 CON__Q14CN4-1;CON__Q3SY84;CON__Q9R0H5 1;1;1 1;1;1 1;1;1 ;; 3 1 1 1 1 1 1 1.6 1.6 1.6 55.877 511 511;523;524 0 6.1238 1.6 0 0 1 + 5 1 True 1 1 1 1

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/combined/txt/summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/combined/txt/summary.txt Sat Jul 20 05:01:05 2019 -0400

[

@@ -0,0 +1,3 @@
+Raw file Experiment Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS Submitted MS/MS Submitted (SIL) MS/MS Submitted (ISO) MS/MS Submitted (PEAK) MS/MS Identified MS/MS Identified (SIL) MS/MS Identified (ISO) MS/MS Identified (PEAK) MS/MS Identified [%] MS/MS Identified (SIL) [%] MS/MS Identified (ISO) [%] MS/MS Identified (PEAK) [%] Peptide Sequences Identified Peaks Peaks Sequenced Peaks Sequenced [%] Peaks Repeatedly Sequenced Peaks Repeatedly Sequenced [%] Isotope Patterns Isotope Patterns Sequenced Isotope Patterns Sequenced (z>1) Isotope Patterns Sequenced [%] Isotope Patterns Sequenced (z>1) [%] Isotope Patterns Repeatedly Sequenced Isotope Patterns Repeatedly Sequenced [%] Recalibrated Av. Absolute Mass Deviation [ppm] Mass Standard Deviation [ppm] Av. Absolute Mass Deviation [mDa] Mass Standard Deviation [mDa]
+BSA_min_23 BSA_min_23.mzXML Trypsin/P Specific False Oxidation (M) Carbamidomethyl (C) False False 1 1 Standard 19 81 0 111 51 0 60 4 2 0 2 3.6 3.92 NaN 3.33 6 1201 57 4.75 4 7.02 165 39 35 23.64 26.52 10 25.64 + 0.41463 0.43436 0.1789 0.18539
+Total 19 81 0 111 51 0 60 4 2 0 2 3.6 3.92 NaN 3.33 6 1201 165 39 35 23.64 26.52 10 25.64 0.41463 0.43436 0.1789 0.18539

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/single/mqpar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single/mqpar.xml Sat Jul 20 05:01:05 2019 -0400

[

b'@@ -0,0 +1,426 @@\n+<?xml version="1.0" encoding="utf-8"?>\r\n+<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\r\n+ <fastaFiles>\r\n+ <FastaFileInfo>\r\n+ <fastaFilePath>D:\\fasta\\bsa.fasta</fastaFilePath>\r\n+ <identifierParseRule>>([^\\s]*)</identifierParseRule>\r\n+ <descriptionParseRule>>(.*)</descriptionParseRule>\r\n+ <taxonomyParseRule></taxonomyParseRule>\r\n+ <variationParseRule></variationParseRule>\r\n+ <modificationParseRule></modificationParseRule>\r\n+ <taxonomyId></taxonomyId>\r\n+ </FastaFileInfo>\r\n+ </fastaFiles>\r\n+ <fastaFilesProteogenomics>\r\n+ </fastaFilesProteogenomics>\r\n+ <fastaFilesFirstSearch>\r\n+ </fastaFilesFirstSearch>\r\n+ <fixedSearchFolder></fixedSearchFolder>\r\n+ <andromedaCacheSize>350000</andromedaCacheSize>\r\n+ <advancedRatios>True</advancedRatios>\r\n+ <pvalThres>0.005</pvalThres>\r\n+ <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\r\n+ <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\r\n+ <rtShift>False</rtShift>\r\n+ <separateLfq>False</separateLfq>\r\n+ <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\r\n+ <lfqRequireMsms>True</lfqRequireMsms>\r\n+ <decoyMode>revert</decoyMode>\r\n+ <boxCarMode>all</boxCarMode>\r\n+ <includeContaminants>True</includeContaminants>\r\n+ <maxPeptideMass>4600</maxPeptideMass>\r\n+ <epsilonMutationScore>True</epsilonMutationScore>\r\n+ <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\r\n+ <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\r\n+ <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\r\n+ <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\r\n+ <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\r\n+ <minScoreModifiedPeptides>40</minScoreModifiedPeptides>\r\n+ <secondPeptide>True</secondPeptide>\r\n+ <matchBetweenRuns>False</matchBetweenRuns>\r\n+ <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\r\n+ <matchBetweenRunsFdr>False</matchBetweenRunsFdr>\r\n+ <dependentPeptides>False</dependentPeptides>\r\n+ <dependentPeptideFdr>0</dependentPeptideFdr>\r\n+ <dependentPeptideMassBin>0</dependentPeptideMassBin>\r\n+ <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\r\n+ <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\r\n+ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\r\n+ <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\r\n+ <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\r\n+ <msmsConnection>False</msmsConnection>\r\n+ <ibaq>False</ibaq>\r\n+ <top3>False</top3>\r\n+ <independentEnzymes>False</independentEnzymes>\r\n+ <useDeltaScore>False</useDeltaScore>\r\n+ <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\r\n+ <taxonomyLevel>Species</taxonomyLevel>\r\n+ <avalon>False</avalon>\r\n+ <nModColumns>3</nModColumns>\r\n+ <ibaqLogFit>False</ibaqLogFit>\r\n+ <razorProteinFdr>True</razorProteinFdr>\r\n+ <deNovoSequencing>False</deNovoSequencing>\r\n+ <deNovoVarMods>True</deNovoVarMods>\r\n+ <massDifferenceSearch>False</massDifferenceSearch>\r\n+ <isotopeCalc>False</isotopeCalc>\r\n+ <writePeptidesForSpectrumFile></writePeptidesForSpectrumFile>\r\n+ <intensityPredictionsFile>\r\n+ </intensityPredictionsFile>\r\n+ <minPepLen>7</minPepLen>\r\n+ <psmFdrCrosslink>0.01</psmFdrCrosslink>\r\n+ <peptideFdr>0.01</peptideFdr>\r\n+ <proteinFdr>0.01</proteinFdr>\r\n+ <siteFdr>0.01</siteFdr>\r\n+ <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\r\n+ <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\r\n+ <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\r\n+ <minPeptides>1</minPeptides>\r\n+ <minRazorPeptides>1</minRazorPeptides>\r\n+ <minUniquePeptides>0</minUniquePeptides>\r\n+ <useCounterparts>False</useCou'..b'terval>100</TopxInterval>\r\n+ <HigherCharges>True</HigherCharges>\r\n+ <IncludeWater>True</IncludeWater>\r\n+ <IncludeAmmonia>True</IncludeAmmonia>\r\n+ <DependentLosses>True</DependentLosses>\r\n+ <Recalibration>False</Recalibration>\r\n+ </msmsParams>\r\n+ </msmsParamsArray>\r\n+ <fragmentationParamsArray>\r\n+ <fragmentationParams>\r\n+ <Name>CID</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>HCD</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>ETD</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>PQD</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>ETHCD</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>ETCID</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>UVPD</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ <fragmentationParams>\r\n+ <Name>Unknown</Name>\r\n+ <Connected>False</Connected>\r\n+ <ConnectedScore0>1</ConnectedScore0>\r\n+ <ConnectedScore1>1</ConnectedScore1>\r\n+ <ConnectedScore2>1</ConnectedScore2>\r\n+ <InternalFragments>False</InternalFragments>\r\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\r\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\r\n+ </fragmentationParams>\r\n+ </fragmentationParamsArray>\r\n+</MaxQuantParams>\r\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de test-data/template.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/template.xml Sat Jul 20 05:01:05 2019 -0400

b'@@ -0,0 +1,428 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n+ <fastaFiles>\n+ <FastaFileInfo>\n+ <fastaFilePath></fastaFilePath>\n+ <identifierParseRule>>(.*)</identifierParseRule>\n+ <descriptionParseRule></descriptionParseRule>\n+ <taxonomyParseRule></taxonomyParseRule>\n+ <variationParseRule></variationParseRule>\n+ <modificationParseRule></modificationParseRule>\n+ <taxonomyId></taxonomyId>\n+ </FastaFileInfo>\n+ </fastaFiles>\n+ <fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+ <fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+ <fixedSearchFolder></fixedSearchFolder>\n+ <andromedaCacheSize>350000</andromedaCacheSize>\n+ <advancedRatios>True</advancedRatios>\n+ <pvalThres>0.005</pvalThres>\n+ <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\n+ <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\n+ <rtShift>False</rtShift>\n+ <separateLfq>False</separateLfq>\n+ <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+ <lfqRequireMsms>True</lfqRequireMsms>\n+ <decoyMode>revert</decoyMode>\n+ <boxCarMode>all</boxCarMode>\n+ <includeContaminants>True</includeContaminants>\n+ <maxPeptideMass>4600</maxPeptideMass>\n+ <epsilonMutationScore>True</epsilonMutationScore>\n+ <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+ <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+ <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+ <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+ <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+ <minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+ <secondPeptide>True</secondPeptide>\n+ <matchBetweenRuns>False</matchBetweenRuns>\n+ <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+ <matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+ <dependentPeptides>False</dependentPeptides>\n+ <dependentPeptideFdr>0</dependentPeptideFdr>\n+ <dependentPeptideMassBin>0</dependentPeptideMassBin>\n+ <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+ <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+ <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+ <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+ <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+ <msmsConnection>False</msmsConnection>\n+ <ibaq>False</ibaq>\n+ <top3>False</top3>\n+ <independentEnzymes>False</independentEnzymes>\n+ <useDeltaScore>False</useDeltaScore>\n+ <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+ <taxonomyLevel>Species</taxonomyLevel>\n+ <avalon>False</avalon>\n+ <nModColumns>3</nModColumns>\n+ <ibaqLogFit>False</ibaqLogFit>\n+ <razorProteinFdr>True</razorProteinFdr>\n+ <deNovoSequencing>False</deNovoSequencing>\n+ <deNovoVarMods>True</deNovoVarMods>\n+ <massDifferenceSearch>False</massDifferenceSearch>\n+ <isotopeCalc>False</isotopeCalc>\n+ <writePeptidesForSpectrumFile></writePeptidesForSpectrumFile>\n+ <intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+ <minPepLen>7</minPepLen>\n+ <psmFdrCrosslink>0.01</psmFdrCrosslink>\n+ <peptideFdr>0.01</peptideFdr>\n+ <proteinFdr>0.01</proteinFdr>\n+ <siteFdr>0.01</siteFdr>\n+ <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+ <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+ <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+ <minPeptides>1</minPeptides>\n+ <minRazorPeptides>1</minRazorPeptides>\n+ <minUniquePeptides>0</minUniquePeptides>\n+ <useCounterparts>False</useCounterparts>\n+ <advancedSiteIntensities>True</advancedSiteIntensities>\n+ <customProteinQuantification>Fa'..b'nceInPpm>\n+ <Deisotope>False</Deisotope>\n+ <Topx>8</Topx>\n+ <TopxInterval>100</TopxInterval>\n+ <HigherCharges>True</HigherCharges>\n+ <IncludeWater>True</IncludeWater>\n+ <IncludeAmmonia>True</IncludeAmmonia>\n+ <DependentLosses>True</DependentLosses>\n+ <Recalibration>False</Recalibration>\n+ </msmsParams>\n+ </msmsParamsArray>\n+ <fragmentationParamsArray>\n+ <fragmentationParams>\n+ <Name>CID</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>HCD</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>ETD</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>PQD</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>ETHCD</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>ETCID</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>UVPD</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ <fragmentationParams>\n+ <Name>Unknown</Name>\n+ <Connected>False</Connected>\n+ <ConnectedScore0>1</ConnectedScore0>\n+ <ConnectedScore1>1</ConnectedScore1>\n+ <ConnectedScore2>1</ConnectedScore2>\n+ <InternalFragments>False</InternalFragments>\n+ <InternalFragmentWeight>1</InternalFragmentWeight>\n+ <InternalFragmentAas>KRH</InternalFragmentAas>\n+ </fragmentationParams>\n+ </fragmentationParamsArray>\n+</MaxQuantParams>\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de unimod.xml
--- a/unimod.xml Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,15140 +0,0 @@\n-\xef\xbb\xbf<?xml version="1.0" encoding="utf-8"?>\n-\n-\n-\n-<umod:unimod xmlns:umod="http://www.unimod.org/xmlns/schema/unimod_2"\n- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n- xsi:schemaLocation="http://www.unimod.org/xmlns/schema/unimod_2 http://www.unimod.org/xmlns/schema/unimod_2/unimod_2.xsd"\n- majorVersion="2"\n- minorVersion="0">\n- <umod:elements>\n- <umod:elem title="H" full_name="Hydrogen" avge_mass="1.00794" mono_mass="1.007825035"/>\n- <umod:elem title="2H" full_name="Deuterium" avge_mass="2.014101779"\n- mono_mass="2.014101779"/>\n- <umod:elem title="Li" full_name="Lithium" avge_mass="6.941" mono_mass="7.016003"/>\n- <umod:elem title="C" full_name="Carbon" avge_mass="12.0107" mono_mass="12"/>\n- <umod:elem title="13C" full_name="Carbon13" avge_mass="13.00335483"\n- mono_mass="13.00335483"/>\n- <umod:elem title="N" full_name="Nitrogen" avge_mass="14.0067" mono_mass="14.003074"/>\n- <umod:elem title="15N" full_name="Nitrogen15" avge_mass="15.00010897"\n- mono_mass="15.00010897"/>\n- <umod:elem title="O" full_name="Oxygen" avge_mass="15.9994" mono_mass="15.99491463"/>\n- <umod:elem title="18O" full_name="Oxygen18" avge_mass="17.9991603" mono_mass="17.9991603"/>\n- <umod:elem title="F" full_name="Fluorine" avge_mass="18.9984032" mono_mass="18.99840322"/>\n- <umod:elem title="Na" full_name="Sodium" avge_mass="22.98977" mono_mass="22.9897677"/>\n- <umod:elem title="P" full_name="Phosphorous" avge_mass="30.973761" mono_mass="30.973762"/>\n- <umod:elem title="S" full_name="Sulfur" avge_mass="32.065" mono_mass="31.9720707"/>\n- <umod:elem title="Cl" full_name="Chlorine" avge_mass="35.453" mono_mass="34.96885272"/>\n- <umod:elem title="K" full_name="Potassium" avge_mass="39.0983" mono_mass="38.9637074"/>\n- <umod:elem title="Ca" full_name="Calcium" avge_mass="40.078" mono_mass="39.9625906"/>\n- <umod:elem title="Fe" full_name="Iron" avge_mass="55.845" mono_mass="55.9349393"/>\n- <umod:elem title="Ni" full_name="Nickel" avge_mass="58.6934" mono_mass="57.9353462"/>\n- <umod:elem title="Zn" full_name="Zinc" avge_mass="65.409" mono_mass="63.9291448"/>\n- <umod:elem title="Se" full_name="Selenium" avge_mass="78.96" mono_mass="79.9165196"/>\n- <umod:elem title="Br" full_name="Bromine" avge_mass="79.904" mono_mass="78.9183361"/>\n- <umod:elem title="Ag" full_name="Silver" avge_mass="107.8682" mono_mass="106.905092"/>\n- <umod:elem title="Hg" full_name="Mercury" avge_mass="200.59" mono_mass="201.970617"/>\n- <umod:elem title="Au" full_name="Gold" avge_mass="196.96655" mono_mass="196.966543"/>\n- <umod:elem title="I" full_name="Iodine" avge_mass="126.90447" mono_mass="126.904473"/>\n- <umod:elem title="Mo" full_name="Molybdenum" avge_mass="95.94" mono_mass="97.9054073"/>\n- <umod:elem title="Cu" full_name="Copper" avge_mass="63.546" mono_mass="62.9295989"/>\n- <umod:elem title="e" full_name="electron" avge_mass="0.000549" mono_mass="0.000549"/>\n- <umod:elem title="B" full_name="Boron" avge_mass="10.811" mono_mass="11.0093055"/>\n- <umod:elem title="As" full_name="Arsenic" avge_mass="74.9215942" mono_mass="74.9215942"/>\n- </umod:elements>\n- <umod:modifications>\n- <umod:mod title="Acetyl" full_name="Acetylation" username_of_poster="unimod"\n- group_of_poster="admin"\n- date_time_posted="2002-08-19 19:17:11"\n- date_time_modified="2008-02-15 05:20:02"\n- approved="1"\n- record_id="1">\n- <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational"\n- '..b'element symbol="H" number="1"/>\n- <umod:element symbol="P" number="1"/>\n- <umod:element symbol="O" number="3"/>\n- </umod:brick>\n- <umod:brick title="Sulf" full_name="Sulfate" mono_mass="79.95681459000001"\n- avge_mass="80.0632">\n- <umod:element symbol="S" number="1"/>\n- <umod:element symbol="O" number="3"/>\n- </umod:brick>\n- <umod:brick title="Pent" full_name="Pentose" mono_mass="132.0422588" avge_mass="132.11462">\n- <umod:element symbol="C" number="5"/>\n- <umod:element symbol="H" number="8"/>\n- <umod:element symbol="O" number="4"/>\n- </umod:brick>\n- <umod:brick title="Li" full_name="Lithium" mono_mass="7.016003" avge_mass="6.941">\n- <umod:element symbol="Li" number="1"/>\n- </umod:brick>\n- <umod:brick title="13C" full_name="Carbon 13" mono_mass="13.00335483"\n- avge_mass="13.00335483">\n- <umod:element symbol="13C" number="1"/>\n- </umod:brick>\n- <umod:brick title="15N" full_name="Nitrogen 15" mono_mass="15.00010897"\n- avge_mass="15.00010897">\n- <umod:element symbol="15N" number="1"/>\n- </umod:brick>\n- <umod:brick title="Cl" full_name="Chlorine" mono_mass="34.96885272" avge_mass="35.453">\n- <umod:element symbol="Cl" number="1"/>\n- </umod:brick>\n- <umod:brick title="K" full_name="Potassium" mono_mass="38.9637074" avge_mass="39.0983">\n- <umod:element symbol="K" number="1"/>\n- </umod:brick>\n- <umod:brick title="Ca" full_name="Calcium" mono_mass="39.9625906" avge_mass="40.078">\n- <umod:element symbol="Ca" number="1"/>\n- </umod:brick>\n- <umod:brick title="Fe" full_name="Iron" mono_mass="55.9349393" avge_mass="55.845">\n- <umod:element symbol="Fe" number="1"/>\n- </umod:brick>\n- <umod:brick title="Ni" full_name="Nickel" mono_mass="57.9353462" avge_mass="58.6934">\n- <umod:element symbol="Ni" number="1"/>\n- </umod:brick>\n- <umod:brick title="Zn" full_name="Zinc" mono_mass="63.9291448" avge_mass="65.409">\n- <umod:element symbol="Zn" number="1"/>\n- </umod:brick>\n- <umod:brick title="Br" full_name="Bromine" mono_mass="78.9183361" avge_mass="79.904">\n- <umod:element symbol="Br" number="1"/>\n- </umod:brick>\n- <umod:brick title="Ag" full_name="Silver" mono_mass="106.905092" avge_mass="107.8682">\n- <umod:element symbol="Ag" number="1"/>\n- </umod:brick>\n- <umod:brick title="Hg" full_name="Mercury" mono_mass="201.970617" avge_mass="200.59">\n- <umod:element symbol="Hg" number="1"/>\n- </umod:brick>\n- <umod:brick title="Au" full_name="Gold" mono_mass="196.966543" avge_mass="196.96655">\n- <umod:element symbol="Au" number="1"/>\n- </umod:brick>\n- <umod:brick title="I" full_name="Iodine" mono_mass="126.904473" avge_mass="126.90447">\n- <umod:element symbol="I" number="1"/>\n- </umod:brick>\n- <umod:brick title="Mo" full_name="Molybdenum" mono_mass="97.9054073" avge_mass="95.94">\n- <umod:element symbol="Mo" number="1"/>\n- </umod:brick>\n- <umod:brick title="Cu" full_name="Copper" mono_mass="62.9295989" avge_mass="63.546">\n- <umod:element symbol="Cu" number="1"/>\n- </umod:brick>\n- <umod:brick title="Hep" full_name="Heptose" mono_mass="192.06338820000002"\n- avge_mass="192.16658">\n- <umod:element symbol="C" number="7"/>\n- <umod:element symbol="H" number="12"/>\n- <umod:element symbol="O" number="6"/>\n- </umod:brick>\n- <umod:brick title="B" full_name="Boron" mono_mass="11.0093055" avge_mass="10.811">\n- <umod:element symbol="B" number="1"/>\n- </umod:brick>\n- <umod:brick title="As" full_name="Arsenic" mono_mass="74.9215942" avge_mass="74.9215942">\n- <umod:element symbol="As" number="1"/>\n- </umod:brick>\n- </umod:mod_bricks>\n-</umod:unimod>\n\\ No newline at end of file\n'

diff -r d4b6c9eae635 -r 8bac3cc5c5de update.sh
--- a/update.sh Fri May 10 17:22:51 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,35 +0,0 @@
-#!/bin/bash
-
-LICENSE_FILE=LICENSE
-# Ensure repository contains license file.
-if [ ! -e "$LICENSE_FILE" ];
-then
-    wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE"
-fi
-
-# Run repository specific update actions.
-if [ -f update_repo.sh ];
-then
-    ./update_repo.sh
-fi
-
-wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md
-
-# Create repository README
-if [ ! -e README_REPO.md ];
-then
-    echo "TODO: Document this tool repository." > README_REPO.md
-fi
-cat README_REPO.md README_GALAXYP.md > README.md
-
-
-# If version file exists, update all tools to this version
-VERSION_FILE=version
-if [ -e "$VERSION_FILE" ];
-then
-    VERSION=`cat $VERSION_FILE`
-
-    # Replace tool version in each tool XML file   `
-    find -iname "*xml" -exec sed -i'' -e '0,/version="$.\+$"/s/version="$.\+$"/version="'$VERSION'"/1g' {} \;
-
-fi