Mercurial > repos > workflow4metabolomics > ms2snoop
annotate MS2snoop.xml @ 6:77abacd33c31 draft
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
| author | workflow4metabolomics |
|---|---|
| date | Fri, 30 Sep 2022 16:18:56 +0000 |
| parents | 78d5a12406c2 |
| children | 2a1f120a6874 |
| rev | line source |
|---|---|
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
2 <description> |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
3 MS1/MS2 spectra and associated adducts extraction and cleaning |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
4 </description> |
|
2
a35fde23940e
planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
workflow4metabolomics
parents:
1
diff
changeset
|
5 <macros> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
6 <import>macros.xml</import> |
|
2
a35fde23940e
planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
workflow4metabolomics
parents:
1
diff
changeset
|
7 </macros> |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
8 <edam_topics> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
9 <edam_topic>topic_0091</edam_topic> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
10 <edam_topic>topic_3370</edam_topic> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
11 </edam_topics> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
12 <edam_operations> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
13 <edam_operation>operation_3803</edam_operation> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
14 <edam_operation>operation_3860</edam_operation> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
15 </edam_operations> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
16 <requirements> |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
17 <requirement type="package" version="4.1.3">r-base</requirement> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
18 <requirement type="package" version="1.7.1">r-optparse</requirement> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
19 <requirement type="package" version="4.9.15">sirius-csifingerid</requirement> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
20 <requirement type="package" version="3.0">zip</requirement> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
21 </requirements> |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
22 <stdio> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
23 <exit_code range="1" level="fatal" description="Missing parameter error" /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
24 <exit_code range="2" level="fatal" description="Bad parameter's value" /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
25 <exit_code range="3" level="fatal" description="Missing input file" /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
26 <exit_code range="4:254" level="fatal" description="Unknown error" /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
27 <exit_code range="255" level="fatal" description="No any result to output" /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
28 <regex match="Error in\s+.*:\s+.*" /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
29 </stdio> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
30 <version_command> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
31 <![CDATA[ |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
32 @COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' --version | head -n 1 |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
33 ]]> |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
34 </version_command> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
35 <command> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
36 <![CDATA[ |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
37 @COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
38 --output '$frag_result_txt' |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
39 --compounds '$compound_txt' |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
40 --fragments '$peaklist_frag_tsv' |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
41 --precursors '$peaklist_preco_tsv' |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
42 --tolmz '$tolmz' |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
43 --tolrt '$tolrt' |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
44 --seuil_ra '$seuil_ra' |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
45 --mzdecimal '$mzdecimal' |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
46 --r_threshold '$r_threshold' |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
47 --min_number_scan '$min_number_scan' |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
48 --ionization '$sirius.ionization' |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
49 --fragment_match_delta '$sirius.fragment_match_delta' |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
50 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit' |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
51 $advenced.pdf |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
52 $advenced.debug |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
53 $advenced.verbose |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
54 ]]> |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
55 </command> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
56 <inputs> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
57 <param argument="--compound_txt" type="data" format="tabular,csv,tsv" |
|
2
a35fde23940e
planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
workflow4metabolomics
parents:
1
diff
changeset
|
58 label="list of compounds" |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
59 help="The table must fit the format: compound_name, inchikey, [elemcomposition], mz, rtsec." |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
60 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
61 <param argument="--peaklist_frag_tsv" type="data" format="tabular,csv,tsv" |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
62 label="MSpurity fragments file" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
63 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
64 <param argument="--peaklist_preco_tsv" type="data" format="tabular,csv,tsv" |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
65 label="MSpurity precursors file" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
66 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
67 <param argument="--tolmz" type="float" min="0.0001" max="10" value="0.01" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
68 label="MZ Tolerence" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
69 help="M/z tolerance to determine if a precursor matches a compound" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
70 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
71 <param argument="--tolrt" type="integer" min="0" max="30" value="20" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
72 label="RT Tolerence (in seconds)" |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
73 help="Retention time tolerance to determine if a precursor matches a compound" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
74 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
75 <param argument="--seuil_ra" type="float" min="0" max="1" value="0.05" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
76 label="R-Pearson correlation threshold used to filter fragments" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
77 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
78 <param argument="--mzdecimal" type="integer" min="0" max="5" value="3" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
79 label="Number of decimal to output M/z values with" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
80 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
81 <param argument="--r_threshold" type="float" min="0" value="0.85" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
82 label=" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
83 Minimun correlation with absolute intensity value to reach |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
84 for a fragment to be considered as valid. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
85 In PDF generation, invalid fragments will be |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
86 displayed in grey. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
87 " |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
88 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
89 <param argument="--min_number_scan" type="integer" min="0" max="25" value="8" |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
90 label="Present in at least X scan" |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
91 help="Mininum scan number in which a fragment must be found, to be kept." |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
92 /> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
93 |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
94 <section title="Sirius Parameters" name="sirius"> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
95 <param argument="--ionization" type="select" optional="true" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
96 label="Which ionization" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
97 help="Select the ionization to use in sirius" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
98 > |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
99 <option value="[M+H]+" selected="true">[M+H]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
100 <option value="[M-H]-">[M-H]-</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
101 <option value="[M+?]+">[M+?]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
102 <option value="[M+K]+">[M+K]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
103 <option value="[M+Na]+">[M+Na]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
104 <option value="[M+H-H2O]+">[M+H-H2O]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
105 <option value="[M+H-H4O2]+">[M+H-H4O2]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
106 <option value="[M+NH4]+">[M+NH4]+</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
107 <option value="[M+Cl]-">[M+Cl]-</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
108 <option value="[M-H2O-H]-">[M-H2O-H]-</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
109 <option value="[M+Br]-">[M+Br]-</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
110 </param> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
111 |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
112 <param argument="--fragment_match_delta" type="float" min="0" max="25" value="10" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
113 label="Fragment match delta" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
114 help=" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
115 Delta that determines if a fragment found by sirius |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
116 is linked to a certain M/z value. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
117 Zero means all fragments found by sirius will be |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
118 associated even when M/z difference is aberant. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
119 " |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
120 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
121 <param argument="--fragment_match_delta_unit" type="select" optional="true" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
122 label="Delta unit" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
123 help="Select the unit of the fragment match delta" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
124 > |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
125 <option value="ppm" selected="true">PPM</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
126 <option value="mz">M/z</option> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
127 </param> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
128 </section> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
129 |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
130 <section title="Advenced Options" name="advenced"> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
131 <param argument="--pdf" type="boolean" truevalue="--pdf_path '$pdf_output'" falsevalue="" value="" optional="true" |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
132 label="Output PDF" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
133 help="The tool will output some pdf in a zip file" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
134 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
135 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" value="" optional="true" |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
136 label="Verbose logs" |
|
2
a35fde23940e
planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
workflow4metabolomics
parents:
1
diff
changeset
|
137 help="The tool will print more logs" |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
138 /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
139 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" value="" optional="true" |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
140 label="Debug statements" |
|
2
a35fde23940e
planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
workflow4metabolomics
parents:
1
diff
changeset
|
141 help="The tool will print debug statements" |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
142 /> |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
143 </section> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
144 </inputs> |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
145 <outputs> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
146 <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
147 <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}"> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
148 <filter>advenced['pdf']</filter> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
149 </data> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
150 </outputs> |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
151 <tests> |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
152 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
153 <!-- Regular test with no option --> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
154 <param name="compound_txt" value="compounds_pos.txt" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
155 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
156 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
157 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
158 <assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
159 <expand macro="has_regular_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
160 <expand macro="has_not_verbose_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
161 <expand macro="has_not_debug_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
162 </assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
163 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
164 |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
165 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
166 <!-- Regular files with verbose output --> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
167 <param name="compound_txt" value="compounds_pos.txt" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
168 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
169 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
170 <param name="verbose" value="--verbose" /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
171 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
172 <assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
173 <expand macro="has_regular_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
174 <expand macro="has_verbose_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
175 <expand macro="has_not_debug_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
176 </assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
177 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
178 |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
179 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
180 <!-- Regular test with debug outputs --> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
181 <param name="compound_txt" value="compounds_pos.txt" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
182 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
183 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
184 <param name="debug" value="--debug" /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
185 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
186 <assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
187 <expand macro="has_smol_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
188 <expand macro="has_debug_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
189 <expand macro="has_not_verbose_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
190 </assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
191 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
192 |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
193 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
194 <!-- Regular test with both verbose and debug outputs --> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
195 <param name="compound_txt" value="compounds_pos.txt" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
196 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
197 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
198 <param name="debug" value="--debug" /> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
199 <param name="verbose" value="--verbose" /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
200 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
201 <assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
202 <expand macro="has_smol_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
203 <expand macro="has_debug_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
204 <expand macro="has_smol_verbose_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
205 </assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
206 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
207 |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
208 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
209 <!-- |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
210 This test mixes tsv, csv, and so, and ms2snoop is expected |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
211 handle them like usual. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
212 --> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
213 <param name="compound_txt" value="compounds_pos.csv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
214 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
215 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
216 <param name="verbose" value="--verbose" /> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
217 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
218 <assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
219 <expand macro="has_regular_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
220 <expand macro="has_verbose_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
221 <expand macro="has_not_debug_stdout"/> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
222 </assert_stdout> |
|
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
223 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
224 |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
225 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
226 <!-- |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
227 This test contains smaller datasets. This is the "regular" |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
228 smol test, to prepare further smolah tests. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
229 --> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
230 <param name="ionization" value="[M+?]+" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
231 <param name="mzdecimal" value="3" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
232 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
233 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
234 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
235 <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
236 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
237 |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
238 <test> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
239 <!-- |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
240 Test for pdf generation |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
241 --> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
242 <param name="pdf" value="True" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
243 <param name="ionization" value="[M+?]+" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
244 <param name="mzdecimal" value="3" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
245 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
246 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
247 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
248 <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
249 </test> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
250 |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
251 <test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
252 <!-- |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
253 test for delta in ppm |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
254 --> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
255 <param name="ionization" value="[M+?]+" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
256 <param name="mzdecimal" value="3" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
257 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
258 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
259 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
260 <param name="fragment_match_delta" value="8.542" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
261 <output name="frag_result_txt" file="smol/out-smol-delta-8.542.tsv" /> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
262 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
263 |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
264 <test> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
265 <!-- |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
266 test for delta in m/z |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
267 --> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
268 <param name="ionization" value="[M+?]+" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
269 <param name="mzdecimal" value="3" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
270 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
271 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
272 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
273 <param name="fragment_match_delta" value="0.05" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
274 <param name="fragment_match_delta_unit" value="mz" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
275 <output name="frag_result_txt" file="smol/out-smol-delta-0.05mz.tsv" /> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
276 </test> |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
277 |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
278 <!-- === expected to fail tests === --> |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
279 <test expect_exit_code="2" expect_failure="true"> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
280 <!-- |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
281 This test uses old format for molecules file. |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
282 Is is expected to fail |
|
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
283 --> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
284 <param name="compound_txt" value="compounds_pos_old_format.txt" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
285 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
286 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
287 <assert_stderr> |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
288 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" /> |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
289 </assert_stderr> |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
290 </test> |
|
5
78d5a12406c2
planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
workflow4metabolomics
parents:
4
diff
changeset
|
291 |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
292 </tests> |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
293 <help> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
294 <![CDATA[ |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
295 @AUTHORS@ |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
296 |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
297 ============== |
|
3
c68c94865667
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
workflow4metabolomics
parents:
2
diff
changeset
|
298 MS2 validation |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
299 ============== |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
300 |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
301 ----------- |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
302 Description |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
303 ----------- |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
304 |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
305 MS2snoop use results of msPurity to find spectra of standards listed in |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
306 a compounds file. Check the fragments and precursor using correlation of |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
307 among the different scans of fragments |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
308 |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
309 ----------------- |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
310 Workflow position |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
311 ----------------- |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
312 |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
313 -------------- |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
314 Upstream tools |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
315 -------------- |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
316 |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
317 +-------------------------+-----------------+--------+------------+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
318 | Name | output file | format | parameter | |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
319 +=========================+=================+========+============+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
320 | msPurity.purityA | NA | TSV | NA | |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
321 +-------------------------+-----------------+--------+------------+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
322 | msPurity.frag4feature | NA | TSV | NA | |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
323 +-------------------------+-----------------+--------+------------+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
324 |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
325 ---------------- |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
326 Downstream tools |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
327 ---------------- |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
328 |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
329 +-------------------------+-----------------+--------+------------+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
330 | Name | output file | format | parameter | |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
331 +=========================+=================+========+============+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
332 | NA | NA | NA | NA | |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
333 +-------------------------+-----------------+--------+------------+ |
|
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
334 |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
335 |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
336 ----------- |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
337 Input files |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
338 ----------- |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
339 |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
340 +----------------------------------------------+------------+ |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
341 | Parameter : num + label | Format | |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
342 +===========================+==================+============+ |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
343 | Input from msPurity Precursor | TSV,CSV | |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
344 +----------------------------------------------+------------+ |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
345 | Input from msPurity fragment | TSV,CSV | |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
346 | Input compounds file to search in precursor | | |
|
1
df2672c37732
planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
workflow4metabolomics
parents:
0
diff
changeset
|
347 +----------------------------------------------+------------+ |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
348 | and fragment (Name + m/z + ret Time) | TSV,CSV | |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
349 +----------------------------------------------+------------+ |
|
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
350 |
|
4
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
351 @PARAMETERS@ |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
352 @OUTPUTS@ |
|
856001213966
planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
workflow4metabolomics
parents:
3
diff
changeset
|
353 @CHANGELOG@ |
|
6
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
354 ]]> |
|
77abacd33c31
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
workflow4metabolomics
parents:
5
diff
changeset
|
355 </help> |
|
0
91a3242fd67f
"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
parents:
diff
changeset
|
356 </tool> |