Mercurial > repos > iuc > msaboot

annotate msaboot.xml @ 0:48b414c7d38e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
author iuc
date Mon, 19 Feb 2018 14:07:33 -0500
parents
children 9625ddf6eed5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
2 <tool id="msaboot" name="MSABOOT" version="@VERSION@">
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
3 <description>Output PHYLIP file with bootstrapped multiple sequence alignment data</description>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
4 <macros>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
5 <token name="@VERSION@">0.1.0</token>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
6 </macros>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
7 <requirements>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
8 <requirement type="package" version="@VERSION@">msaboot</requirement>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
9 </requirements>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
10 <version_command>msaboot --version</version_command>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
11 <command detect_errors="aggressive">
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
12 <![CDATA[
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
13 msaboot -i '$input' -n $number -o '$output'
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
14 #if $save_logfile:
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
15 > '$log' 2>&1
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
16 #end if
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
17 ]]>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
18 </command>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
19 <inputs>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
20 <param name="input" format="fasta" type="data" label="FASTA input file" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
21 <param name="number" type="integer" value="1" min="1" label="Specify the number of bootstrapping replicates to generate." />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
22 <param name="save_logfile" type="boolean" truevalue="" falsevalue="" label="Output log file" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
23 </inputs>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
24 <outputs>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
25 <data name="output" format="phylip" label="${tool.name} on ${on_string}:out.phylip" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
26 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_msabootpl_run.txt">
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
27 <filter>save_logfile</filter>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
28 </data>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
29 </outputs>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
30 <tests>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
31 <test>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
32 <param name="input" value="msa.fasta" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
33 <param name="number" value="10" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
34 <param name="save_logfile" value="true" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
35 <output name="log" file="log.txt" ftype="txt" compare="contains" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
36 <output name="output" file="out.phylip" ftype="phylip" compare="contains" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
37 </test>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
38 </tests>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
39 <help>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
40 <![CDATA[
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
41
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
42 ===========
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
43 Description
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
44 ===========
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
45
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
46 .. class:: infomark
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
47
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
48 A tool for creating bootstrapping replicates from Multiple Sequence Alignment data.
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
49
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
50 .. _msaboot: https://github.com/phac-nml/msaboot
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
51
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
52 -----
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
53
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
54 -----
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
55 Input
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
56 -----
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
57 Input file location of FASTA file containing Multiple Sequence Alignment data(-i)
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
58
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
59 ----------
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
60 Parameters
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
61 ----------
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
62 Number of bootstrapping replicates (-n)
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
63
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
64 ------
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
65 Output
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
66 ------
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
67
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
68 This tool produces two output files, one of which is optional (the log file).
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
69
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
70 (A) The bootstrapped replicates in Phylip format.
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
71
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
72 (B) The optional log file, containing information about the msaboot run to bootstrap the multiple sequence alignment data.
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
73
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
74 ]]>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
75 </help>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
76 <citations>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
77 <citation type="bibtex">
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
78 @misc{GitHubmsaboot,
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
79 title = {msaboot},
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
80 publisher = {phac-nml},
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
81 journal = {GitHub repository},
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
82 url = {https://github.com/phac-nml/msaboot},
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
83 }
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
84 </citation>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
85 </citations>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
iuc
parents:
diff changeset
86 </tool>