Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/wolf_psort.xml @ 16:7de64c8b258d draft
Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
author | peterjc |
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date | Wed, 18 Sep 2013 06:16:58 -0400 |
parents | 6365217cd3de |
children | e6cc27d182a8 |
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15:6abd809cefdd | 16:7de64c8b258d |
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1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.4"> | 1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.6"> |
2 <description>Eukaryote protein subcellular localization prediction</description> | 2 <description>Eukaryote protein subcellular localization prediction</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 wolf_psort.py $organism 8 $fasta_file $tabular_file | 4 wolf_psort.py $organism "\$NSLOTS" "$fasta_file" "$tabular_file" |
5 ##I want the number of threads to be a Galaxy config option... | 5 ##I want the number of threads to be a Galaxy config option... |
6 ##Set the number of threads in the runner entry in universe_wsgi.ini | |
7 ##which (on SGE at least) will set the $NSLOTS environment variable. | |
8 ##If the environment variable isn't set, get "", and python wrapper | |
9 ##defaults to four threads. | |
6 </command> | 10 </command> |
7 <stdio> | 11 <stdio> |
8 <!-- Anything other than zero is an error --> | 12 <!-- Anything other than zero is an error --> |
9 <exit_code range="1:" /> | 13 <exit_code range="1:" /> |
10 <exit_code range=":-1" /> | 14 <exit_code range=":-1" /> |
82 pero peroxisome 0005777(2) | 86 pero peroxisome 0005777(2) |
83 plas plasma membrane 0005886 | 87 plas plasma membrane 0005886 |
84 vacu vacuolar membrane 0005774(2) | 88 vacu vacuolar membrane 0005774(2) |
85 ====== ===================== ===================== | 89 ====== ===================== ===================== |
86 | 90 |
91 Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of" | |
92 cellular components were also included, up to the specified depth (2 in this case). | |
93 For example, all of the children and grandchildren of "GO:0005856" were | |
94 included as "cysk". | |
95 | |
87 Additionally compound predictions like mito_nucl are also given. | 96 Additionally compound predictions like mito_nucl are also given. |
88 | 97 |
89 | 98 |
90 **Notes** | 99 **Notes** |
91 | 100 |
117 least 10 (c2=='extr' and 10<=c3), and so on. | 126 least 10 (c2=='extr' and 10<=c3), and so on. |
118 | 127 |
119 | 128 |
120 **References** | 129 **References** |
121 | 130 |
122 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai, | 131 If you use this Galaxy tool in work leading to a scientific publication please |
132 cite the following papers: | |
133 | |
134 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
135 Galaxy tools and workflows for sequence analysis with applications | |
136 in molecular plant pathology. PeerJ 1:e167 | |
137 http://dx.doi.org/10.7717/peerj.167 | |
138 | |
139 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007). | |
123 WoLF PSORT: Protein Localization Predictor. | 140 WoLF PSORT: Protein Localization Predictor. |
124 Nucleic Acids Research, 35(S2), W585-W587, 2007. | 141 Nucleic Acids Research, 35(S2), W585-W587. |
125 http://dx.doi.org/10.1093/nar/gkm259 | 142 http://dx.doi.org/10.1093/nar/gkm259 |
126 | 143 |
127 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai. | 144 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006). |
128 Protein Subcellular Localization Prediction with WoLF PSORT. | 145 Protein Subcellular Localization Prediction with WoLF PSORT. |
129 Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006. | 146 Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48. |
130 | 147 |
131 http://wolfpsort.org | 148 See also http://wolfpsort.org |
132 | 149 |
150 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
151 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | |
133 </help> | 152 </help> |
134 </tool> | 153 </tool> |