Mercurial > repos > sblanck > mpagenomics
comparison segmentation.xml @ 4:3fcbb8030fcc draft
"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" /> |