Mercurial > repos > workflow4metabolomics > ms2snoop

comparison MS2snoop.xml @ 2:a35fde23940e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
author workflow4metabolomics
date Wed, 08 Jun 2022 12:37:53 +0000
parents df2672c37732
children c68c94865667
comparison
equal deleted inserted replaced
1:df2672c37732 2:a35fde23940e
1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> 1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <macros>
3 <token name="@TOOL_VERSION@">1.0.1</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
6 <description> 2 <description>
7 MS1/MS2 spectra and associated adducts extraction and cleaning 3 MS1/MS2 spectra and associated adducts extraction and cleaning
8 </description> 4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">1.0.1</token>
7 <token name="@VERSION_SUFFIX@">1</token>
8 </macros>
9 <edam_topics> 9 <edam_topics>
10 <edam_topic>topic_0091</edam_topic> 10 <edam_topic>topic_0091</edam_topic>
11 <edam_topic>topic_3370</edam_topic> 11 <edam_topic>topic_3370</edam_topic>
12 </edam_topics> 12 </edam_topics>
13 <edam_operations> 13 <edam_operations>
46 $advenced.verbose 46 $advenced.verbose
47 ]]> 47 ]]>
48 </command> 48 </command>
49 <inputs> 49 <inputs>
50 <param 50 <param
51 argument="--compound_txt"
51 type="data" 52 type="data"
52 format="tabular,csv" 53 format="tabular,csv"
53 argument="--compound_txt" 54 label="list of compounds"
54 label="list of compounds : col1=Name of molecule, col2=m/z, col3=retention time" 55 help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time"
55 /> 56 />
56 <param 57 <param
58 argument="--peaklist_frag_tsv"
57 type="data" 59 type="data"
58 format="tabular,csv" 60 format="tabular,csv"
59 argument="--peaklist_frag_tsv"
60 label="MSpurity fragments file" 61 label="MSpurity fragments file"
61 /> 62 />
62 <param 63 <param
64 argument="--peaklist_preco_tsv"
63 type="data" 65 type="data"
64 format="tabular,csv" 66 format="tabular,csv"
65 argument="--peaklist_preco_tsv"
66 label="MSpurity precursors file" 67 label="MSpurity precursors file"
67 /> 68 />
68 <param 69 <param
70 argument="--tolmz"
69 type="float" 71 type="float"
70 min="0.0001" 72 min="0.0001"
71 max="10" 73 max="10"
72 value="0.01" 74 value="0.01"
73 label="MZ Tolerence" 75 label="MZ Tolerence"
74 argument="--tolmz" 76 />
75 /> 77 <param
76 <param 78 argument="--tolrt"
77 type="integer" 79 type="integer"
78 min="0" 80 min="0"
79 max="30" 81 max="30"
80 value="20" 82 value="20"
81 label="RT Tolerence" 83 label="RT Tolerence"
82 argument="--tolrt" 84 />
83 /> 85 <param
84 <param 86 argument="--seuil_ra"
85 type="float" 87 type="float"
86 min="0" 88 min="0"
87 max="1" 89 max="1"
88 value="0.05" 90 value="0.05"
89 label="r pearson correlation threshold between precursor and fragment absolute intensity" 91 label="r pearson correlation threshold between precursor and fragment absolute intensity"
90 argument="--seuil_ra" 92 />
91 /> 93 <param
92 <param 94 argument="--mzdecimal"
93 type="integer" 95 type="integer"
94 min="0" 96 min="0"
95 max="5" 97 max="5"
96 value="0" 98 value="0"
97 label="nb decimal for mz" 99 label="nb decimal for mz"
98 argument="--mzdecimal" 100 />
99 /> 101 <param
100 <param 102 argument="--r_threshold"
101 type="float" 103 type="float"
102 min="0" 104 min="0"
103 value="0.85" 105 value="0.85"
104 label="fragment absolute intensity" 106 label="fragment absolute intensity"
105 argument="--r_threshold" 107 />
106 /> 108 <param
107 <param 109 argument="--min_number_scan"
108 type="integer" 110 type="integer"
109 min="0" 111 min="0"
110 max="25" 112 max="25"
111 value="8" 113 value="8"
112 label="Present in at least X scan" 114 label="Present in at least X scan"
113 argument="--min_number_scan"
114 help="fragments are kept if they are found in a minimum number of scans" 115 help="fragments are kept if they are found in a minimum number of scans"
115 /> 116 />
116 <section title="Advenced Options" name="advenced"> 117 <section title="Advenced Options" name="advenced">
117 <param 118 <param
119 argument="--verbose"
118 type="boolean" 120 type="boolean"
119 value="" 121 value=""
122 optional="true"
120 label="Verbose logs" 123 label="Verbose logs"
121 argument="--verbose" 124 help="The tool will print more logs"
122 truevalue="--verbose" 125 truevalue="--verbose"
123 falsevalue="" 126 falsevalue=""
124 help="The tool will print more logs"
125 optional="true"
126 /> 127 />
127 <param 128 <param
129 argument="--debug"
128 type="boolean" 130 type="boolean"
129 value="" 131 value=""
132 optional="true"
130 label="Debug statements" 133 label="Debug statements"
131 argument="--debug" 134 help="The tool will print debug statements"
132 truevalue="--debug" 135 truevalue="--debug"
133 falsevalue="" 136 falsevalue=""
134 help="The tool will print debug statements"
135 optional="true"
136 /> 137 />
137 </section> 138 </section>
138 </inputs> 139 </inputs>
139 <outputs> 140 <outputs>
140 <data 141 <data