Mercurial > repos > lain > xseekerpreparator

comparison galaxy/tools/LC-MSMS/XSeekerPreparator.xml @ 4:8cc9fc8eacac draft

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" master branch Updating"
author lain
date Thu, 17 Dec 2020 12:54:10 +0000
parents fa97d16330be
children 4d50e9324082
comparison
equal deleted inserted replaced
3:fa97d16330be 4:8cc9fc8eacac
8 <edam_operation>operation_1812</edam_operation> 8 <edam_operation>operation_1812</edam_operation>
9 <edam_operation>operation_0335</edam_operation> 9 <edam_operation>operation_0335</edam_operation>
10 </edam_operations> 10 </edam_operations>
11 11
12 <requirements> 12 <requirements>
13 <requirement type="set_environment">R_SCRIPT</requirement> 13 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
14 <requirement type="package" version="4.0.0">R</requirement> 14 <requirement type="package">bioconductor-camera</requirement>
15 <requirement type="package" version="1.6.6">optparse</requirement> 15 <requirement type="package" version="2.29.2">git</requirement>
16 <requirement type="package" version="3.10.2">xcms</requirement> 16 <requirement type="package" version="4.0">R</requirement>
17 <requirement type="package" version="1.2.1">blob</requirement> 17 <requirement type="package" version="1.2.1">r-blob</requirement>
18 <requirement type="package" version="0.9.4">fst</requirement> 18 <requirement type="package" version="1.1.0">r-dbi</requirement>
19 <requirement type="package" version="1.4.0">stringr</requirement> 19 <requirement type="package" version="0.9.4">r-fst</requirement>
20 <requirement type="package">DBModelR</requirement> 20 <requirement type="package" version="1.6.6">r-optparse</requirement>
21 <requirement type="package" version="1.4.0">r-stringr</requirement>
22 <requirement type="package" version="0.3.4">r-purrr</requirement>
23 <requirement type="package" version="2.2.1">r-rsqlite</requirement>
24 <requirement type="package" version="0.1.0">r-dbmodelr</requirement>
21 </requirements> 25 </requirements>
22
23 <stdio> 26 <stdio>
24 27
25 <exit_code 28 <exit_code
26 range="1" 29 range="1"
27 level="warning" 30 level="warning"
35 /> 38 />
36 39
37 </stdio> 40 </stdio>
38 41
39 <version_command> 42 <version_command>
40 $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v 43 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
41 </version_command> 44 </version_command>
42 45
43 <command> 46 <command>
44 <![CDATA[ 47 <![CDATA[
45 $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' 48 Rscript '$__tool_directory__/XSeekerPreparator.R'
46 49
47 -P 50 -P
48 51
49 --input '$input' 52 --input '$input'
50 --output '$output' 53 --output '$output'
51 54
52 #if $samples.selected 55 #if $samples.selected
53 --samples '${",".join(samples.selected)}' 56 --samples '${",".join($samples.selected)}'
54 #end if 57 #end if
55 58
56 #if $database.archetypes 59 #if $database.archetypes
57 --archetype '${",".join($database.archetypes)}' 60 --archetype '${",".join($database.archetypes)}'
58 #end if 61 #end if
153 </inputs> 156 </inputs>
154 157
155 158
156 <outputs> 159 <outputs>
157 <data format="sqlite" name="output" /> 160 <data format="sqlite" name="output" />
161 <!-- <data format="xseeker.sqlite" name="output" /> -->
158 </outputs> 162 </outputs>
159 163
160 <configfiles> 164 <configfiles>
161 <configfile name="base_config"> 165 <configfile name="base_config">
162 tryCatch({ 166 tryCatch({