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comparison segmentation.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="segmentation" name="Segmentation and calling" force_history_refresh="True" version="1.1.0"> 1 <tool id="segmentation" name="Segmentation and calling" version="1.2.0">
2 <description>of a previously normalized signal</description> 2 <description>of a previously normalized signal</description>
3 <requirement type="package" version="1.1.2">mpagenomics</requirement> 3 <requirements>
4 <container type="docker">sblanck/mpagenomicsdependencies</container>
5 </requirements>
4 <command> 6 <command>
5 <![CDATA[ 7 <![CDATA[
6 Rscript 8 Rscript
7 ${__tool_directory__}/segmentation.R 9 ${__tool_directory__}/segmentation.R
8 #if $signalType.signal == "CN": 10 #if $signalType.signal == "CN":
11 #else 13 #else
12 --nbcall '3' 14 --nbcall '3'
13 --cellularity '1.0' 15 --cellularity '1.0'
14 #end if 16 #end if
15 --input '$input' 17 --input '$input'
16 --new_file_path '$__new_file_path__' 18 --new_file_path '$output.extra_files_path'
17 --outputlog '$outputlog' 19 --outputlog '$outputlog'
18 --output '$output' 20 --output '$output'
19 --log '$log' 21 --log '$log'
20 --outputgraph '$outputgraph' 22 --outputgraph '$outputgraph'
21 --graph '$graph' 23 --graph '$graph'
61 <outputs> 63 <outputs>
62 <data format="scr" name="output" label="segmentation of ${input.name}" /> 64 <data format="scr" name="output" label="segmentation of ${input.name}" />
63 <data format="log" name="log" label="log of segmentation of ${input.name}"> 65 <data format="log" name="log" label="log of segmentation of ${input.name}">
64 <filter>outputlog == "TRUE"</filter> 66 <filter>outputlog == "TRUE"</filter>
65 </data> 67 </data>
66 <data format="pdf" name="graph" label="graph of segmentation of ${input.name}"> 68 <data format="zip" name="graph" label="graph of segmentation of ${input.name}">
67 <filter>outputgraph == "TRUE"</filter> 69 <filter>outputgraph == "TRUE"</filter>
68 </data> 70 </data>
69 </outputs> 71 </outputs>
70 <stdio> 72 <stdio>
71 <exit_code range="1:" level="fatal" description="See logs for more details" /> 73 <exit_code range="1:" level="fatal" description="See logs for more details" />