Mercurial > repos > computational-metabolomics > mspurity_createdatabase

comparison macros.xml @ 6:2f71b3495221 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:27:21 +0000
parents 3ec6fd8e4c17
children 0cc6b67dccb8
comparison
equal deleted inserted replaced
5:3ec6fd8e4c17 6:2f71b3495221
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">