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comparison ms2pf_it.xml @ 1:7e3085fc60c1 draft default tip

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master branch Updating
author lain
date Wed, 30 Aug 2023 14:21:18 +0000
parents b58b229c4cbf
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0:b58b229c4cbf 1:7e3085fc60c1
1 <tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description> 2 <description>
3 adds you MS spectrum to peakforest. 3 adds you MS spectrum to peakforest.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@TOOL_VERSION@">1.2.1</token>
7 <import>macros.xml</import> 7 <token name="@VERSION_SUFFIX@">0</token>
8 </macros> 8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="3.10">python</requirement> 10 <container type="docker">quay.io/pfem/ms2peakforest:@TOOL_VERSION@</container>
11 <requirement type="package">pyyaml</requirement> 11 </requirements>
12 </requirements> 12 <entry_points>
13 <entry_points> 13 <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True">
14 <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True"> 14 <port>8000</port>
15 <port>8000</port> 15 <url>/</url>
16 <url>/</url> 16 </entry_point>
17 </entry_point> 17 </entry_points>
18 </entry_points> 18 <version_command>
19 <version_command>
20 <![CDATA[ 19 <![CDATA[
21 python3 '$__tool_directory__/server.py' --version | head -n 1 20 python3 '$__tool_directory__/server.py' --version | head -n 1
22 ]]> 21 ]]>
23 </version_command> 22 </version_command>
24 <command> 23 <command><![CDATA[
25 @MS2PF_COMMON_CMD@ 24 cd /ms2pf
26 </command> 25 && python3 '$__tool_directory__/server.py'
27 <inputs> 26 --input '${','.join(map(str, $input))}'
28 <expand macro="ms2pf_inputs" /> 27 --raw-metadata '${advanced.raw_metadata_sep.join(str(i.name) for i in $input)}'
29 </inputs> 28 --raw-metadata-sep '$advanced.raw_metadata_sep'
30 <outputs> 29 --method '$method'
31 <data name="ms2pfout" format="txt" 30 --peakforest-url '$peakforest_url'
32 label="${tool.name} on ${','.join(i.name for i in $input)}" 31 --peakforest-token '$peakforest_token'
33 /> 32 --spectrum-type '$spectrum_type'
34 <data name="json_output" format="json" 33 --sample-type '$sample_type'
35 label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json" 34 --sample-type '$sample_type'
36 > 35 #if $advanced.rt_min != 0.0 and $advanced.rt_max != 0.0
37 <filter>do_output_json</filter> 36 --rt-min '$advanced.rt_min'
38 </data> 37 --rt-max '$advanced.rt_max'
39 </outputs> 38 #else
40 <tests> 39 --rt-min ''
41 </tests> 40 --rt-max ''
41 #end if
42 --polarity '$polarity'
43 --name '$advanced.name'
44 #if $advanced.do_output_json:
45 --output-json '$json_output'
46 #end if
47 $advanced.verbose
48 $advanced.debug
49 ]]>
50 </command>
51 <inputs>
52 <param argument="--input" type="data" multiple="true" format="tabular,csv,tsv"
53 label="list of files to process"
54 help="A data collection from fragnot or a single file from ms2snoop."
55 />
56 <param argument="--peakforest-url" type="select"
57 label="PeakForest instance"
58 help="Determines on which pf instance we push data"
59 refresh_on_change="true"
60 >
61 <option value="https://alpha.peakforest.org">alpha</option>
62 <option value="https://nightly.peakforest.org">nightly</option>
63 <option value="https://metabohub.peakforest.org">metabohub</option>
64 </param>
65 <param argument="--peakforest-token" type="text"
66 label="PeakForest token"
67 help="Please provide you api token for this instance"
68 />
69 <param argument="--spectrum-type" type="select"
70 label="Spectrum Type"
71 help="Spectrum Type"
72 refresh_on_change="true"
73 >
74 <option value="LC_MS">LC-MS</option>
75 <option value="LC_MSMS">LC-MSMS</option>
76 <option value="GC_MS">GC-MS</option>
77 </param>
78
79 <param argument="--method" type="select"
80 label="Chromatography Method"
81 dynamic_options="[list(x.values())+[False] for x in __import__('json').loads(__import__('urllib').request.urlopen(peakforest_url+'/webapp/resources/json/list-'+ ('lc' if spectrum_type == 'LC_MS' else 'lc-msms') +'-methods.json?token='+peakforest_token).read())['methods']]"
82 >
83 </param>
84
85 <param argument="--sample-type" type="select"
86 label="Sample Type"
87 help="Sample Type"
88 >
89 <option value="compound-ref">Compound Ref</option>
90 <option value="compound-mix">Compound Mix</option>
91 </param>
92 <param argument="--polarity" type="select"
93 label="polarity"
94 help="polarity"
95 >
96 <option value="positive">positive</option>
97 <option value="negative">negative</option>
98 <option value="neutral">neutral</option>
99 </param>
100 <section name="advanced">
101 <param argument="--name" type="text"
102 label="name"
103 help="name, or names separated by commas"
104 />
105 <param argument="--rt-min" type="float" value="0.0"
106 label="Min RT"
107 help="The default min RT to set"
108 />
109 <param argument="--rt-max" type="float" value="0.0"
110 label="Max RT"
111 help="The default max RT to set"
112 />
113 <param argument="--raw-metadata-sep" type="text" value="XXX"
114 label="Files names separator"
115 help="Select a/some character·s that are not in any file name."
116 />
117 <param name="do_output_json" type="boolean"
118 label="Produce JSON"
119 help="
120 Select this option to output a json file of the
121 resulting processing.
122 "
123 />
124 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue=""
125 label="Activate debug logs"
126 help="Select to produce more detailed logs."
127 />
128 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue=""
129 label="Activate verbose logs"
130 help="Select to produce more logs."
131 />
132 </section>
133 </inputs>
134 <outputs>
135 <data name="ms2pfout" format="txt"
136 label="${tool.name} on ${','.join(i.name for i in $input)}"
137 />
138 <data name="json_output" format="json"
139 label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json"
140 >
141 <filter>do_output_json</filter>
142 </data>
143 </outputs>
144 <tests>
145 </tests>
42 <help> 146 <help>
43 <![CDATA[ 147 <![CDATA[
44 .. class:: infomark 148 .. class:: infomark
45 149
46 **Authors** Lain Pavot (lain.pavot@inrae.fr) 150 **Authors** Lain Pavot (lain.pavot@inrae.fr)
134 238
135 -------------- 239 --------------
136 Changelog/News 240 Changelog/News
137 -------------- 241 --------------
138 242
243 1.2.0
244 | Version from images hosted on quay.io.
139 1.0.0 245 1.0.0
140 | First version, published on the toolshed. 246 | First version, published on the toolshed.
141 247
142 ]]> 248 ]]>
143 </help> 249 </help>
144 </tool> 250 </tool>