Mercurial > repos > lain > ms_to_peakforest_it
annotate ms2pf_it.xml @ 1:7e3085fc60c1 draft default tip
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author | lain |
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date | Wed, 30 Aug 2023 14:21:18 +0000 |
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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 | 2 <description> |
3 adds you MS spectrum to peakforest. | |
4 </description> | |
5 <macros> | |
6 <token name="@TOOL_VERSION@">1.2.1</token> | |
7 <token name="@VERSION_SUFFIX@">0</token> | |
8 </macros> | |
9 <requirements> | |
10 <container type="docker">quay.io/pfem/ms2peakforest:@TOOL_VERSION@</container> | |
11 </requirements> | |
12 <entry_points> | |
13 <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True"> | |
14 <port>8000</port> | |
15 <url>/</url> | |
16 </entry_point> | |
17 </entry_points> | |
18 <version_command> | |
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19 <![CDATA[ |
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20 python3 '$__tool_directory__/server.py' --version | head -n 1 |
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21 ]]> |
1 | 22 </version_command> |
23 <command><![CDATA[ | |
24 cd /ms2pf | |
25 && python3 '$__tool_directory__/server.py' | |
26 --input '${','.join(map(str, $input))}' | |
27 --raw-metadata '${advanced.raw_metadata_sep.join(str(i.name) for i in $input)}' | |
28 --raw-metadata-sep '$advanced.raw_metadata_sep' | |
29 --method '$method' | |
30 --peakforest-url '$peakforest_url' | |
31 --peakforest-token '$peakforest_token' | |
32 --spectrum-type '$spectrum_type' | |
33 --sample-type '$sample_type' | |
34 --sample-type '$sample_type' | |
35 #if $advanced.rt_min != 0.0 and $advanced.rt_max != 0.0 | |
36 --rt-min '$advanced.rt_min' | |
37 --rt-max '$advanced.rt_max' | |
38 #else | |
39 --rt-min '' | |
40 --rt-max '' | |
41 #end if | |
42 --polarity '$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> | |
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146 <help> |
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147 <![CDATA[ |
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148 .. class:: infomark |
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149 |
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150 **Authors** Lain Pavot (lain.pavot@inrae.fr) |
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151 |
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152 .. class:: infomark |
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153 |
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154 --------------------------------------------------- |
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155 |
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156 ============== |
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157 MS2 validation |
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158 ============== |
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159 |
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160 ----------- |
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161 Description |
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162 ----------- |
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163 |
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164 |
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165 ----------------- |
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166 Workflow position |
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167 ----------------- |
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168 |
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169 -------------- |
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170 Upstream tools |
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171 -------------- |
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172 |
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173 +-------------------------+-----------------+--------+------------+ |
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174 | Name | output file | format | parameter | |
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175 +=========================+=================+========+============+ |
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176 | ms2snoop | tsv | TSV | NA | |
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177 +-------------------------+-----------------+--------+------------+ |
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178 | abinitfragnot | tsv | TSV | NA | |
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179 +-------------------------+-----------------+--------+------------+ |
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180 |
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181 ---------------- |
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182 Downstream tools |
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183 ---------------- |
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184 |
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185 +-------------------------+-----------------+--------+------------+ |
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186 | Name | output file | format | parameter | |
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187 +=========================+=================+========+============+ |
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188 | NA | NA | NA | NA | |
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189 +-------------------------+-----------------+--------+------------+ |
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190 |
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191 |
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192 ----------- |
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193 Input files |
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194 ----------- |
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195 |
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196 +----------------------------------------------+------------+ |
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197 | Parameter : num + label | Format | |
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198 +===========================+==================+============+ |
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199 | Output from ms2snoop or fragnot | TSV,CSV | |
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200 +----------------------------------------------+------------+ |
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201 |
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202 ---------- |
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203 Parameters |
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204 ---------- |
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205 |
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206 input |
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207 | The file to process. Should contain spectra with mz, intensities and |
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208 annotations |
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209 |
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210 method |
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211 | The method parameter tells which method was used. The value will |
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212 be the default value in the peakforest form. |
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213 |
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214 peakforest-url |
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215 | The peakforest-url parameter tells which instance of peakforest to |
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216 interact with |
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217 |
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218 scan_type |
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219 | The scan_type parameter which kind of scan was used. The value will |
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220 be the default value in the peakforest form. |
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221 |
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222 polarity |
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223 | The polarity parameter which polarity was used. The value will |
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224 be the default value in the peakforest form. |
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225 |
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226 name |
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227 | The name parameter provides names each spectra. |
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228 |
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229 |
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230 ------------ |
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231 Output files |
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232 ------------ |
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233 |
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234 There is not output file. When you run this tool, keep waiting until the |
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235 « click here to display » link appears. |
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236 |
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237 Click on the link to display peakforest form. |
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238 |
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239 -------------- |
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240 Changelog/News |
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241 -------------- |
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242 |
1 | 243 1.2.0 |
244 | Version from images hosted on quay.io. | |
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245 1.0.0 |
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246 | First version, published on the toolshed. |
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247 |
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248 ]]> |
1 | 249 </help> |
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250 </tool> |