Mercurial > repos > dereeper > sniplay
comparison Rooting/rooting.xml @ 4:10627af23f10 draft
planemo upload
author | gandres |
---|---|
date | Tue, 15 Dec 2015 05:18:02 -0500 |
parents | 345f88a8f483 |
children | ec22fcacb66c |
comparison
equal
deleted
inserted
replaced
3:345f88a8f483 | 4:10627af23f10 |
---|---|
1 <tool id="sniplay_rooting" name="Rooting" version="1.1"> | 1 <tool id="sniplay_rooting" name="Rooting" version="1.0.2"> |
2 | 2 |
3 <!-- [REQUIRED] Tool description displayed after the tool name --> | 3 <!-- [REQUIRED] Tool description displayed after the tool name --> |
4 <description> Midpoint rooting of newick tree </description> | 4 <description> Midpoint rooting of newick tree </description> |
5 | 5 |
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> |
7 <requirements> | 7 <requirements> |
8 <requirement type="binary">perl</requirement> | 8 <requirement type="binary">perl</requirement> |
9 <requirement type="package">Rootings_54.jar</requirement> | 9 <requirement type="package">Rootings_54.jar</requirement> |
10 </requirements> | 10 </requirements> |
11 | |
12 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
13 <stdio> | |
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
15 <exit_code range="1:" level="fatal" /> | |
16 </stdio> | |
17 | |
11 | 18 |
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | 19 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> |
13 <version_command> | 20 <version_command> |
14 <!-- | 21 <!-- |
15 tool_binary -v | 22 tool_binary -v |
21 Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log | 28 Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log |
22 </command> | 29 </command> |
23 | 30 |
24 <!-- [REQUIRED] Input files and tool parameters --> | 31 <!-- [REQUIRED] Input files and tool parameters --> |
25 <inputs> | 32 <inputs> |
26 <param name="filein" type="data" format="txt" optional="false" label="Newick tree input" /> | 33 <param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" /> |
27 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> | 34 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> |
28 </inputs> | 35 </inputs> |
29 | 36 |
30 <!-- [REQUIRED] Output files --> | 37 <!-- [REQUIRED] Output files --> |
31 <outputs> | 38 <outputs> |
32 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> | 39 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> |
33 <data name="fileout" type="data" format="txt" label="${fileout_label}" /> | 40 <data name="fileout" type="data" format="txt" label="${fileout_label}" /> |
34 </outputs> | 41 </outputs> |
35 | 42 |
36 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
37 <stdio> | |
38 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
39 <exit_code range="1:" level="fatal" /> | |
40 </stdio> | |
41 | |
42 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | 43 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> |
43 <tests> | 44 <tests> |
44 <!-- [HELP] Test files have to be in the ~/test-data directory --> | 45 <!-- [HELP] Test files have to be in the ~/test-data directory --> |
45 | 46 |
46 <test> | 47 <test> |
47 <param name="filein" value="newick" /> | 48 <param name="filein" value="rooting-newick" /> |
48 <output name="fileout" file="out_tree" /> | 49 <output name="fileout" file="rooting-out_tree" /> |
49 <output name="fileout_log" file="out_tree.log" /> | |
50 </test> | 50 </test> |
51 | 51 |
52 <!-- [HELP] Multiple tests can be defined with different parameters --> | 52 <!-- [HELP] Multiple tests can be defined with different parameters --> |
53 <!-- | 53 <!-- |
54 <test> | 54 <test> |