Skip to content

Commit aa6f733

Browse files
TomnlTomnl
authored
v1.12.2+galaxy1 (#38)
* Update grpPeaklist reference * Add include_adducts_custom to createMSP.xml * Add include_adducts_all to createMSP.R * Change output of flagRemove to tabular * Update custom adduct handling * Make sure custom adducts not called when not used * Update custom adducts * added validator for custom adducts * add validator * refine createmsp adduct combo
1 parent 242de15 commit aa6f733

File tree

6 files changed

+162
-11
lines changed

6 files changed

+162
-11
lines changed

‎tools/msPurity/createDatabase.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@
2929
#end if
3030
3131
#if $grp_peaklist_opt.grp_peaklist_opt=="yes"
32-
--grp_peaklist='$grp_peaklist'
32+
--grpPeaklist='$grp_peaklist'
3333
#end if
3434
3535
]]></command>

‎tools/msPurity/createMSP.R‎

Lines changed: 23 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,7 @@ option_list <- list(
1515
make_option("--intensity_ra",type="character"),
1616
make_option("--include_adducts",type="character"),
1717
make_option("--msp_schema",type="character"),
18+
make_option("--include_adducts_custom",type="character", default=""),
1819
make_option("--out_dir",type="character", default=".")
1920
)
2021
opt <- parse_args(OptionParser(option_list=option_list))
@@ -66,17 +67,33 @@ if (is.null(opt$xcms_groupids)){
6667
xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
6768
}
6869

70+
71+
72+
73+
74+
if (is.null(opt$include_adducts_custom)){
75+
include_adducts_custom <- ''
76+
}else{
77+
include_adducts_custom <- opt$include_adducts_custom
78+
}
79+
80+
6981
if (opt$include_adducts=='None'){
7082
include_adducts <- ''
7183
}else{
7284
include_adducts <- opt$include_adducts
73-
include_adducts <- gsub("__ob__", "[", include_adducts)
74-
include_adducts <- gsub("__cb__", "]", include_adducts)
75-
include_adducts <- trimws(include_adducts)
85+
}
7686

77-
include_adducts <- gsub(",", " ", include_adducts)
87+
include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="")
88+
89+
include_adducts_all <- gsub("^,", "", include_adducts_all)
90+
include_adducts_all <- gsub(",$", "", include_adducts_all)
91+
92+
include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
93+
include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
94+
include_adducts_all <- trimws(include_adducts_all)
95+
include_adducts_all <- gsub(",", " ", include_adducts_all)
7896

79-
}
8097

8198

8299
if(is.null(opt$filter)){
@@ -96,7 +113,7 @@ msPurity::createMSP(pa,
96113
xcms_groupids = xcms_groupids,
97114
filter = filter,
98115
intensity_ra=opt$intensity_ra,
99-
include_adducts=include_adducts,
116+
include_adducts=include_adducts_all,
100117
msp_schema=opt$msp_schema)
101118

102119
print('msp created')

‎tools/msPurity/createMSP.xml‎

Lines changed: 25 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,9 @@
2727
--msp_schema $msp_schema
2828
--intensity_ra $intensity_ra
2929
--include_adducts $include_adducts
30+
#if $include_adducts_custom
31+
--include_adducts_custom "$include_adducts_custom"
32+
#end if
3033
3134
--out_dir '.'
3235
]]></command>
@@ -106,8 +109,13 @@
106109
<option value="[M+CH3COO]-" >[M+CH3COO]-</option>
107110
<option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
108111
</param>
112+
<param argument="--include_adducts_custom" type="text" label="Always include the following custom adducts"
113+
help="Additional custom adducts to include, should be comma separated" optional="true">
114+
<expand macro="text-adduct-regex-validator"/>
115+
</param>
116+
109117
<param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
110-
help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue="" />
118+
help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue=""/>
111119

112120
</inputs>
113121
<outputs>
@@ -116,7 +124,7 @@
116124
<tests>
117125

118126
<test>
119-
<!-- 3) Test all average with metadata -->
127+
<!-- Test all average with metadata -->
120128
<param name="method" value="av_all"/>
121129
<param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
122130
<param name="metadata_cond|metadata_select" value="true"/>
@@ -127,6 +135,21 @@
127135
<output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
128136
</test>
129137

138+
<test>
139+
<!-- Test custom adducts average with metadata -->
140+
<param name="method" value="av_all"/>
141+
<param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
142+
<param name="metadata_cond|metadata_select" value="true"/>
143+
<param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
144+
<param name="xcms_group_cond|xcms_group_select" value="true"/>
145+
<param name="xcms_group_cond|xcms_groupids" value="8,12"/>
146+
<param name="metadata_cond|adduct_split" value="true"/>
147+
<param name="include_adducts_custom" value="[M+]+,[M-H]-,[M+TEST SPACE+]+"/>
148+
<output name="createMSP_output" file="createMSP_output_av_all_metadata_custom_adducts.msp"/>
149+
</test>
150+
151+
152+
130153
</tests>
131154
<help><![CDATA[
132155
------------------------------

‎tools/msPurity/flagRemove.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -149,9 +149,9 @@
149149
</conditional>
150150
</inputs>
151151
<outputs>
152-
<data name="peaklist_filtered" format="tsv" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
152+
<data name="peaklist_filtered" format="tabular" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
153153
from_work_dir="peaklist_filtered.tsv" />
154-
<data name="removed_peaks" format="tsv" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
154+
<data name="removed_peaks" format="tabular" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
155155
from_work_dir="removed_peaks.tsv" />
156156
<data name="xset_filtered" format="rdata" label="xset_filtered"
157157
from_work_dir="xset_filtered.RData"/>

‎tools/msPurity/macros.xml‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,9 @@
1616
</requirements>
1717
</xml>
1818

19+
<xml name="text-adduct-regex-validator">
20+
<validator type="regex" message="Value may include alphanumeric characters, white space, commas, +, -, [ or ] ">[A-Za-z0-9,\[\] \+\-]+</validator>
21+
</xml>
1922

2023
<xml name="offsets">
2124
<param argument="--minoffset" type="float" label="minoffset" value="0.5"

‎tools/msPurity/test-data/createMSP_output_av_all_metadata_custom_adducts.msp‎

Lines changed: 108 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,108 @@
1+
RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+NH4]+
2+
MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
3+
AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
4+
isotope [4][M]+
5+
MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+
6+
AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
7+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
8+
AC$MASS_SPECTROMETRY: MS_TYPE MS2
9+
CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
10+
CH$LINK: PUBCHEM CID:5328
11+
CH$NAME Unknown
12+
XCMS groupid (grpid): 12
13+
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2
14+
PK$NUM_PEAK: 2
15+
PK$PEAK: m/z int. rel.int.
16+
112.050884246826 502873.46875 100
17+
126.53768157959 2499.31469726562 0.5
18+
19+
RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+H+NH3]+
20+
MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
21+
AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
22+
isotope [4][M]+
23+
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
24+
AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
25+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
26+
AC$MASS_SPECTROMETRY: MS_TYPE MS2
27+
CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
28+
CH$LINK: PUBCHEM CID:5328
29+
CH$NAME Unknown
30+
XCMS groupid (grpid): 12
31+
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2
32+
PK$NUM_PEAK: 2
33+
PK$PEAK: m/z int. rel.int.
34+
112.050884246826 502873.46875 100
35+
126.53768157959 2499.31469726562 0.5
36+
37+
RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+]+
38+
MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
39+
AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
40+
isotope [4][M]+
41+
MS$FOCUSED_ION: PRECURSOR_TYPE [M+]+
42+
AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
43+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
44+
AC$MASS_SPECTROMETRY: MS_TYPE MS2
45+
CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
46+
CH$LINK: PUBCHEM CID:5328
47+
CH$NAME Unknown
48+
XCMS groupid (grpid): 12
49+
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2
50+
PK$NUM_PEAK: 2
51+
PK$PEAK: m/z int. rel.int.
52+
112.050884246826 502873.46875 100
53+
126.53768157959 2499.31469726562 0.5
54+
55+
RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M-H]-
56+
MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
57+
AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
58+
isotope [4][M]+
59+
MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
60+
AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
61+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
62+
AC$MASS_SPECTROMETRY: MS_TYPE MS2
63+
CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
64+
CH$LINK: PUBCHEM CID:5328
65+
CH$NAME Unknown
66+
XCMS groupid (grpid): 12
67+
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2
68+
PK$NUM_PEAK: 2
69+
PK$PEAK: m/z int. rel.int.
70+
112.050884246826 502873.46875 100
71+
126.53768157959 2499.31469726562 0.5
72+
73+
RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+TEST
74+
MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
75+
AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
76+
isotope [4][M]+
77+
MS$FOCUSED_ION: PRECURSOR_TYPE [M+TEST
78+
AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
79+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
80+
AC$MASS_SPECTROMETRY: MS_TYPE MS2
81+
CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
82+
CH$LINK: PUBCHEM CID:5328
83+
CH$NAME Unknown
84+
XCMS groupid (grpid): 12
85+
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2
86+
PK$NUM_PEAK: 2
87+
PK$PEAK: m/z int. rel.int.
88+
112.050884246826 502873.46875 100
89+
126.53768157959 2499.31469726562 0.5
90+
91+
RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:SPACE+]+
92+
MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
93+
AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
94+
isotope [4][M]+
95+
MS$FOCUSED_ION: PRECURSOR_TYPE SPACE+]+
96+
AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
97+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
98+
AC$MASS_SPECTROMETRY: MS_TYPE MS2
99+
CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
100+
CH$LINK: PUBCHEM CID:5328
101+
CH$NAME Unknown
102+
XCMS groupid (grpid): 12
103+
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2
104+
PK$NUM_PEAK: 2
105+
PK$PEAK: m/z int. rel.int.
106+
112.050884246826 502873.46875 100
107+
126.53768157959 2499.31469726562 0.5
108+

0 commit comments

Comments
 (0)