Mercurial > repos > galaxyp > maxquant

annotate test_mqparam.py @ 4:dcd39bcc7481 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:49:19 -0400
parents
children 37d669de2828
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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1 """Tests for mqparam class. If testing a new MaxQuant version,
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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2 create a new parameter file using '<MAXQUANT_CMD> -c ./mqpar.xml'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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3 """
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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5 import pytest
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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6 import xml.etree.ElementTree as ET
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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7 from mqparam import MQParam, ParamGroup
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8
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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9 TEMPLATE_PATH = './test-data/template.xml'
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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12 def mk_pg_root():
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13 mqpar = ET.parse(TEMPLATE_PATH).getroot()
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14 return mqpar.find('.parameterGroups/parameterGroup')
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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17 class TestParamGroup:
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18 def test_list_param(self):
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19 t = ParamGroup(mk_pg_root())
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20 t.set_list_param('enzymes', ('test 1', 'test 2'))
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21 assert len(t._root.find('enzymes')) == 2
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23 t.set_list_param('variableModifications', ('Oxidation (M)', ))
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24 assert t._root.find('variableModifications')[0].text == 'Oxidation (M)'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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26 with pytest.raises(ValueError):
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27 t.set_list_param('foo', [])
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29 def test_simple_params(self):
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30 t = ParamGroup(mk_pg_root())
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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31 t.set_simple_param('fastLfq', False)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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32 assert t._root.find('.fastLfq').text == 'False'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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34 with pytest.raises(ValueError):
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35 t.set_simple_param('foo', 2)
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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37 def test_silac(self):
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38 t = ParamGroup(mk_pg_root())
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39 t.set_silac(None, None, ('Arg10', 'Lys4'))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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40 assert t._root.find('.maxLabeledAa').text == '2'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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41 assert t._root.find('.multiplicity').text == '2'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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42 assert t._root.find('.labelMods')[1].text == 'Arg10;Lys4'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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43 assert t._root.find('.labelMods')[0].text == ''
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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45 def test_isobaric_label(self):
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46 t = ParamGroup(mk_pg_root())
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47 t.set_isobaric_label('iTRAQ4plex-Lys114', 'iTRAQ4plex-Nter114', 0.3, 1, 1.2, 0, True)
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48
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49 assert len(t._root.find('isobaricLabels')) == 1
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50 assert len(t._root.find('isobaricLabels')[0]) == 7
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51
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52 t.set_isobaric_label('iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115', 0.3, 1.0, 1.2, 0, True)
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53
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54 assert len(t._root.find('isobaricLabels')) == 2
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55
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56 tag_list = [el.tag for el in t._root.find('isobaricLabels')[1]]
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57 assert tag_list == ['internalLabel', 'terminalLabel', 'correctionFactorM2',
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58 'correctionFactorM1', 'correctionFactorP1', 'correctionFactorP2',
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59 'tmtLike']
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61 text_list = [el.text for el in t._root.find('isobaricLabels')[1]]
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62 assert text_list == ['iTRAQ4plex-Lys115', 'iTRAQ4plex-Nter115',
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63 '0.3', '1', '1.2', '0', 'True']
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66 class TestMQParam:
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68 def test_version(self):
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69 t = MQParam(TEMPLATE_PATH)
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70 assert t._root.find('maxQuantVersion').text == '1.6.10.43'
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72 def test_validity_check(self):
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73 design = {'Name': ['Test1', 'Test2'],
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74 'Fraction': ['2', 32767],
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75 'PTM': ['False', 'False'],
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76 'Experiment': ['e1', 'e1'],
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77 'paramGroup': [0, 0]}
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78
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79 assert MQParam._check_validity(design, 2) is None
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81 design['Name'][0] = None
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82 with pytest.raises(Exception):
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83 MQParam._check_validity(design, 2)
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84 design['Name'][0] = 'Test1'
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85
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86 design['Experiment'][0] = ''
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87 with pytest.raises(ValueError):
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88 MQParam._check_validity(design, 2)
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parents:
diff changeset
89 design['Experiment'][0] = 'e1'
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galaxyp
parents:
diff changeset
90
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
91 design['Fraction'][0] = 'foo'
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galaxyp
parents:
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92 with pytest.raises(ValueError):
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galaxyp
parents:
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93 MQParam._check_validity(design, 2)
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galaxyp
parents:
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94
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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95 def test_exp_design(self, tmpdir):
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galaxyp
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96 # default experimental design when None is specified
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galaxyp
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97 t = MQParam(TEMPLATE_PATH)
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galaxyp
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diff changeset
98 design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML'))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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99 assert design['Name'] == ('./Test1.mzXML', './Test2.mzXML')
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
100 assert design['Fraction'] == ('32767', '32767')
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galaxyp
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101
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galaxyp
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102 # valid experimental design
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103 e1 = tmpdir / "e1.txt"
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galaxyp
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104 e1.write('Name\tExperiment\tFraction\tPTM\nTest1\te1\nTest2\te1\t\tfalse')
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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105 t.exp_design = str(e1)
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galaxyp
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diff changeset
106 design = t._make_exp_design((0, 0), ('./Test1.mzXML', './Test2.mzXML'))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
107
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galaxyp
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108 assert design == {'Name': ['./Test1.mzXML', './Test2.mzXML'],
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
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109 'Experiment': ['e1', 'e1'],
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galaxyp
parents:
diff changeset
110 'Fraction': ['32767', '32767'],
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galaxyp
parents:
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111 'PTM': ['False', 'false'],
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galaxyp
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112 'paramGroup': (0, 0)}
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galaxyp
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113
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galaxyp
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114 # invalid header
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galaxyp
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115 e2 = tmpdir / "e2.txt"
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galaxyp
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116 e2.write('Name\tExperiment\tFraction\tPTM\tparamGroup\n')
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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117 t.exp_design = str(e2)
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118
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diff changeset
119 with pytest.raises(Exception):
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120 design = t._make_exp_design(('./Test2.mzXML',), (0,))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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121
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galaxyp
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122 def test_add_infiles(self):
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galaxyp
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123 t = MQParam(TEMPLATE_PATH)
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galaxyp
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124 t.add_infiles([('/path/Test1.mzXML', '/path/Test2.mzXML'),
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galaxyp
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125 ('/path/Test3.mzXML', '/path/Test4.mzXML')])
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galaxyp
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126
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
127 assert [e.text for e in t._root.find('filePaths')] == ['/path/Test1.mzXML',
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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128 '/path/Test2.mzXML',
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galaxyp
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diff changeset
129 '/path/Test3.mzXML',
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galaxyp
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130 '/path/Test4.mzXML']
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131
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132 assert [e.text for e in t._root.find('paramGroupIndices')] == ['0', '0', '1', '1']
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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133 assert t[1]
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134
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galaxyp
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diff changeset
135 def test_translate(self):
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galaxyp
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diff changeset
136 t = MQParam(TEMPLATE_PATH)
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galaxyp
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diff changeset
137 t.add_infiles([('/posix/path/to/Test1.mzXML',
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galaxyp
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diff changeset
138 '/posix/path/to/Test2.mzXML'),
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galaxyp
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diff changeset
139 ('/path/dummy.mzXML',)]) # mqparam is not designed for windows
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
140
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
141 t._root.find('filePaths')[2].text = r'D:\Windows\Path\Test3.mzXML'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
142
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
143 t.translate(('/galaxy/working/Test3.mzXML',
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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144 '/galaxy/working/Test1.mzXML',
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galaxyp
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145 '/galaxy/working/Test2.mzXML',
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galaxyp
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diff changeset
146 '/galaxy/working/Test4.mzXML'))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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147
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galaxyp
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diff changeset
148 assert [e.text for e in t._root.find('filePaths')] == ['/galaxy/working/Test1.mzXML',
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
149 '/galaxy/working/Test2.mzXML',
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galaxyp
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diff changeset
150 '/galaxy/working/Test3.mzXML']
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galaxyp
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diff changeset
151
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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152 def test_fasta_files(self):
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diff changeset
153 t = MQParam(TEMPLATE_PATH)
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galaxyp
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diff changeset
154 t.add_fasta_files(('test1', 'test2'),
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
155 parse_rules={'identifierParseRule': r'>([^\s]*)'})
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
156 assert len(t._root.find('fastaFiles')) == 2
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
157 assert t._root.find('fastaFiles')[0].find("fastaFilePath").text == 'test1'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
158 assert t._root.find('fastaFiles')[0].find("identifierParseRule").text == '>([^\\s]*)'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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159
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galaxyp
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diff changeset
160 def test_simple_param(self):
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galaxyp
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diff changeset
161 t = MQParam(TEMPLATE_PATH)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
162 t.set_simple_param('minUniquePeptides', 4)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
163 assert t._root.find('.minUniquePeptides').text == '4'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents:
diff changeset
164
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galaxyp
parents:
diff changeset
165 with pytest.raises(ValueError):
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
166 t.set_simple_param('foo', 3)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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167
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
168 def test_from_yaml(self, tmpdir):
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galaxyp
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diff changeset
169 conf1 = tmpdir / "conf1.yml"
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galaxyp
parents:
diff changeset
170 conf1.write(r"""
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galaxyp
parents:
diff changeset
171 numThreads: 4
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galaxyp
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diff changeset
172 fastaFiles: [test1.fasta,test2.fasta]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
173 parseRules:
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galaxyp
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174 identifierParseRule: ^>.*\|(.*)\|.*$
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galaxyp
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diff changeset
175 paramGroups:
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176 - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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177 fixedModifications: [mod1,mod2]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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178 lfqMode: 1
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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179 - files: [Test3.mzXML,Test4.mzXML] # paramGroup 1
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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180 labelMods:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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181 - []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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182 - []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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183 - [label1,label2]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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184 """)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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185
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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186 t = MQParam(TEMPLATE_PATH)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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187 t._from_yaml(str(conf1))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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188 assert t['numThreads'] == '4'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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189 assert [child.text for child in t[1]._root.find('labelMods')] == ['', 'label1;label2']
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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190
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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191 def test_write(self, tmpdir):
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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192 yaml_conf = tmpdir / "conf.yml"
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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193 yaml_conf.write(r"""
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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194 numThreads: 4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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195 fastaFiles: [test1.fasta,test2.fasta]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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196 parseRules:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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197 identifierParseRule: ^>.*\|(.*)\|.*$
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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198 paramGroups:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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199 - files: [Test1.mzXML,Test2.mzXML] # paramGroup 0
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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200 fixedModifications: [mod1]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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201 variableModifications: [mod2,mod3]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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202 maxMissedCleavages: 1
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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203 """)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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204 mqpar_out = tmpdir / "mqpar.xml"
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
205
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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206 t = MQParam(TEMPLATE_PATH, yaml=str(yaml_conf))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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207 t.write(str(mqpar_out))
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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208
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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209 test = ET.parse(str(mqpar_out)).getroot()
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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210 assert test.find('numThreads').text == '4'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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211 assert test.find('fastaFiles')[1].find('identifierParseRule').text == '^>.*\\|(.*)\\|.*$'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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212 assert [el.text for el in test.find('parameterGroups')[0].find('variableModifications')] == ['mod2', 'mod3']