Mercurial > repos > computational-metabolomics > mspurity_purityx
comparison macros.xml @ 6:6b9a83e08467 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author | computational-metabolomics |
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date | Thu, 04 Mar 2021 12:25:25 +0000 |
parents | 84b2151fd8f4 |
children | 942e676515fe |
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5:84b2151fd8f4 | 6:6b9a83e08467 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <token name="@TOOL_VERSION@">1.12.2</token> | 3 <token name="@TOOL_VERSION@">1.16.2</token> |
4 <token name="@GALAXY_TOOL_VERSION@">3</token> | 4 <token name="@GALAXY_TOOL_VERSION@">0</token> |
5 | 5 |
6 <xml name="requirements"> | 6 <xml name="requirements"> |
7 <requirements> | 7 <requirements> |
8 <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement> |
9 <requirement type="package" version="1.42.0" >bioconductor-camera</requirement> | 9 <requirement type="package" version="1.46.0" >bioconductor-camera</requirement> |
10 <requirement type="package" version="3.8.0" >bioconductor-xcms</requirement> | 10 <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement> |
11 <requirement type="package" version="1.14.0" >bioconductor-mspuritydata</requirement> | 11 <requirement type="package" version="1.16.0" >bioconductor-mspuritydata</requirement> |
12 <requirement type="package" version="1.6.4">r-optparse</requirement> | 12 <requirement type="package" version="1.6.6">r-optparse</requirement> |
13 <requirement type="package" version="1.1.1">r-rpostgres</requirement> | 13 <requirement type="package" version="1.3.1">r-rpostgres</requirement> |
14 <requirement type="package" version="0.10.17">r-rmysql</requirement> | 14 <requirement type="package" version="0.10.21">r-rmysql</requirement> |
15 <yield /> | 15 <yield /> |
16 </requirements> | 16 </requirements> |
17 </xml> | 17 </xml> |
18 | 18 |
19 <xml name="text-adduct-regex-validator"> | 19 <xml name="text-adduct-regex-validator"> |
21 </xml> | 21 </xml> |
22 | 22 |
23 <xml name="offsets"> | 23 <xml name="offsets"> |
24 <param argument="--minoffset" type="float" label="minoffset" value="0.5" | 24 <param argument="--minoffset" type="float" label="minoffset" value="0.5" |
25 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is | 25 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is |
26 100.0 then the range would be from 999.5 to 100.0"/> | 26 100.0 then the range would be from 99.5 to 100.0"/> |
27 <param argument="--maxoffset" type="float" label="maxoffset" value="0.5" | 27 <param argument="--maxoffset" type="float" label="maxoffset" value="0.5" |
28 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is | 28 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is |
29 100.0 then the range would be from 100.0 to 100.5"/> | 29 100.0 then the range would be from 100.0 to 100.5"/> |
30 </xml> | 30 </xml> |
31 <xml name="general_params"> | 31 <xml name="general_params"> |
32 <param argument="--ilim" type="float" value="0.05" | 32 <param argument="--ilim" type="float" value="0.05" |
33 label="Threshold to remove peaks below x % of the relative intensity of | 33 label="Threshold to remove peaks below x % of the relative intensity of |
34 precursor of interest" | 34 precursor of interest" |
35 help="All peaks less than this percentage of the precursor ion of interest will be | 35 help="All peaks less than this percentage of the precursor ion of interest will be |
36 removed from the purity calculation, default is 5\% (0.05). | 36 removed from the purity calculation, default is 5\% (0.05). |
37 Essentially a noise filter to remove peaks that are thought to have either none or | 37 Essentially a noise filter to remove peaks that are thought to have either none or |
335 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?" | 335 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?" |
336 help="" /> | 336 help="" /> |
337 <when value="true"> | 337 <when value="true"> |
338 <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" > | 338 <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" > |
339 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option> | 339 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option> |
340 <option value="av_inter">Averaged inter spectra</option> | 340 <option value="inter">Averaged inter spectra</option> |
341 <option value="av_intra">Averaged intra spectra </option> | 341 <option value="intra">Averaged intra spectra </option> |
342 <option value="scans">All individual scans</option> | 342 <option value="scans">All individual scans</option> |
343 <option value="NA">Not applicable/defined</option> | 343 <option value="NA">Not applicable/defined</option> |
344 </param> | 344 </param> |
345 </when> | 345 </when> |
346 <when value="false"> | 346 <when value="false"> |