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comparison preprocess.xml @ 4:3fcbb8030fcc draft

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"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author sblanck
date Mon, 12 Apr 2021 14:47:09 +0000
parents 4d539083cf7f
children 4f753bb8681e
comparison
equal deleted inserted replaced
3:94fc6ed13946 4:3fcbb8030fcc
1 <tool id="preprocess" name="Data Normalization" force_history_refresh="True" version="1.1.0"> 1 <tool id="preprocess" name="Data Normalization" version="1.2.0">
2 <requirements> 2 <requirements>
3 <!--requirement type="set_environment">R_SCRIPT_PATH</requirement--> 3 <container type="docker">sblanck/mpagenomicsdependencies</container>
4 <requirement type="package" version="1.1.2">mpagenomics</requirement> 4 </requirements>
5 </requirements> 5
6 <!--command interpreter="python"-->
7 <command> 6 <command>
8 <![CDATA[ 7 <![CDATA[
9 Rscript 8 Rscript
10 ${__tool_directory__}/preprocess.R 9 ${__tool_directory__}/preprocess.R
11 --summary '$summary' 10 --summary '$summary'
12 --new_file_path '$__new_file_path__' 11 --new_file_path '$zipresults.files_path'
13 --inputcdffull_name '$inputcdffull.name' 12 --inputcdffull_name '$inputcdffull.name'
14 --inputufl_name '$inputufl.name' 13 --inputufl_name '$inputufl.name'
15 --inputugp_name '$inputugp.name' 14 --inputugp_name '$inputugp.name'
16 --inputacs_name '$inputacs.name' 15 --inputacs_name '$inputacs.name'
17 --inputcdffull '$inputcdffull' 16 --inputcdffull '$inputcdffull'
26 --tumorcsv 'none' 25 --tumorcsv 'none'
27 #end if 26 #end if
28 --settingsType '$settings.settingsType' 27 --settingsType '$settings.settingsType'
29 --outputgraph '$outputgraph' 28 --outputgraph '$outputgraph'
30 --zipfigures '$zipfigures' 29 --zipfigures '$zipfigures'
30 --zipresults '$zipresults'
31 --outputlog '$outputlog' 31 --outputlog '$outputlog'
32 --log '$log' 32 --log '$log'
33 --user_id '$__user_id__' 33 --user_id '$__user_id__'
34 --input "#for $input in $inputs# $input;$input.name, #end for#" 34 --input "#for $input in $inputs# $input;$input.name, #end for#"
35 ]]> 35 ]]>
36 36
37 </command> 37 </command>
70 <!-- Would like to make this hidden or not appear all together, but 70 <!-- Would like to make this hidden or not appear all together, but
71 variable outputs require a primary dataset. If hidden refresh 71 variable outputs require a primary dataset. If hidden refresh
72 doesn't occur. 72 doesn't occur.
73 --> 73 -->
74 <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" /> 74 <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" />
75 <data format="zip" name="zipfigures" label="figures of normalization of ${datasetName}"> 75 <data format="zip" name="zipresults" label="Results of normalization of ${datasetName}"/>
76 <data format="zip" name="zipfigures" label="Figures of normalization of ${datasetName}">
76 <filter>outputgraph == "TRUE"</filter> 77 <filter>outputgraph == "TRUE"</filter>
77 </data> 78 </data>
78 <data format="log" name="log" label="log of normalization ${datasetName}"> 79 <data format="log" name="log" label="log of normalization ${datasetName}">
79 <filter>outputlog == "TRUE"</filter> 80 <filter>outputlog == "TRUE"</filter>
80 </data> 81 </data>