Mercurial > repos > dereeper > sniplay

comparison Rooting/rooting.xml @ 4:10627af23f10 draft

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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 &amp;&amp; mv ${filein}.rooting.log $fileout_log 28 Rooting.pl -i $filein -o $fileout &amp;&amp; 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>