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comparison Rooting/rooting.xml @ 10:c6640c49fd01 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 09:00:24 -0400
parents 98c37a5d67f4
children 15b23cdde685
comparison
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9:98c37a5d67f4 10:c6640c49fd01
1 <tool id="sniplay_rooting" name="Rooting" version="1.0.3"> 1 <tool id="sniplay_rooting" name="Rooting" version="2.0.0">
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" version="1.6.924">perl-bioperl</requirement>
10 </requirements> 10 </requirements>
11 11
12 <!-- [STRONGLY RECOMMANDED] Exit code rules --> 12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio> 13 <stdio>
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> 14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
28 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 $fileout_log
29 </command> 29 </command>
30 30
31 <!-- [REQUIRED] Input files and tool parameters --> 31 <!-- [REQUIRED] Input files and tool parameters -->
32 <inputs> 32 <inputs>
33 <param name="filein" type="data" format="nwk" optional="false" label="Fasta alignment input" /> 33 <param name="filein" type="data" format="nwk,nhx" optional="false" label="Newick tree input" />
34 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> 34 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
35 </inputs> 35 </inputs>
36 36
37 <!-- [REQUIRED] Output files --> 37 <!-- [REQUIRED] Output files -->
38 <outputs> 38 <outputs>
39 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> 39 <data name="fileout_log" format="txt" label="${fileout_label}.log" />
40 <data name="fileout" type="data" format="nwk" label="${fileout_label}" /> 40 <data name="fileout" format="nwk,nhx" label="${fileout_label}" />
41 </outputs> 41 </outputs>
42 42
43 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 43 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
44 <tests> 44 <tests>
45 <!-- [HELP] Test files have to be in the ~/test-data directory --> 45 <!-- [HELP] Test files have to be in the ~/test-data directory -->
46
47 <test> 46 <test>
48 <param name="filein" value="rooting-newick" /> 47 <param name="filein" value="rooting-newick" />
49 <output name="fileout" file="rooting-out_tree" /> 48 <output name="fileout" file="rooting-out_tree" />
50 </test> 49 </test>
51
52 <!-- [HELP] Multiple tests can be defined with different parameters -->
53 <!--
54 <test>
55 </test>
56 -->
57 </tests> 50 </tests>
58 51
59 <!-- [OPTIONAL] Help displayed in Galaxy --> 52 <!-- [OPTIONAL] Help displayed in Galaxy -->
60 <help> 53 <help><![CDATA[
61
62 54
63 .. class:: infomark 55 .. class:: infomark
64 56
65 **Authors** Jean-François Dufayard, CIRAD, South Green platform 57 **Authors** Jean-François Dufayard, CIRAD, South Green platform
66 58
59 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
67 60
68 .. class:: infomark 61 .. class:: infomark
69 62
70 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. 63 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
71 64
72 .. class:: infomark 65 .. class:: infomark
73 66
74 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr 67 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
75
76 .. class:: infomark
77
78 **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
79 68
80 --------------------------------------------------- 69 ---------------------------------------------------
81
82
83
84 70
85 ======= 71 =======
86 Rooting 72 Rooting
87 ======= 73 =======
88 74
90 Description 76 Description
91 ----------- 77 -----------
92 78
93 Compute a midpoint newick rooted tree. 79 Compute a midpoint newick rooted tree.
94 80
81 ------------
82 Dependencies
83 ------------
84 Bioperl
85 perl-bioperl_ 1.6.924, Conda version
95 86
96 ----------------- 87 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
97 Workflow position
98 -----------------
99
100 **Upstream tool**
101
102 =========== ========================== =======
103 Name output file(s) format
104 =========== ========================== =======
105 fastme Newick tree Newick
106 =========== ========================== =======
107
108
109 88
110 ---------- 89 ----------
111 Input file 90 Input file
112 ---------- 91 ----------
113 92
114 Newick file 93 Newick file
115 94 Input tree file
116 95
117 ---------- 96 ----------
118 Parameters 97 Parameters
119 ---------- 98 ----------
120 99
142 121
143 --------------- 122 ---------------
144 Working example 123 Working example
145 --------------- 124 ---------------
146 125
147 Input files 126 Input file
148 =========== 127 ==========
149 128
150 Newick file 129 Newick file
151 ----------- 130 -----------
152 131
153 :: 132 ::
154 133
155 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... 134 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
156 135
157 136
158 Parameters 137 Parameter
159 ========== 138 =========
160 139
161 Output name -> out tree 140 Output name -> out tree
162 141
163 142
164 Output files 143 Output file
165 ============ 144 ===========
166 145
167 out tree 146 out tree
168 -------- 147 --------
169 148
170 :: 149 ::
171 150
172 (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... 151 (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
173 152
174 153
175 </help> 154 ]]></help>
176 <citations> 155 <citations>
177 <!-- [HELP] As DOI or BibTex entry --> 156 <!-- [HELP] As DOI or BibTex entry -->
178 <citation type="bibtex">@article{Dereeper03062015, 157 <citation type="bibtex">@article{Dereeper03062015,
179 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 158 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
180 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, 159 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},