Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/psortb.xml @ 17:e6cc27d182a8 draft

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Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
author peterjc
date Fri, 21 Nov 2014 08:19:09 -0500
parents 7de64c8b258d
children eb6ac44d4b8e
comparison
equal deleted inserted replaced
16:7de64c8b258d 17:e6cc27d182a8
1 <tool id="Psortb" name="psortb" version="0.0.3"> 1 <tool id="Psortb" name="psortb" version="0.0.5">
2 <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description> 2 <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
3 <!-- If job splitting is enabled, break up the query file into parts --> 3 <!-- If job splitting is enabled, break up the query file into parts -->
4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> 4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
6 <version_command interpreter="python">psortb.py --version</version_command> 6 <version_command interpreter="python">psortb.py --version</version_command>
7 <command interpreter="python"> 7 <command interpreter="python">
8 psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile" 8 psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
9 ##I want the number of threads to be a Galaxy config option...
10 ##Set the number of threads in the runner entry in universe_wsgi.ini
11 ##which (on SGE at least) will set the $NSLOTS environment variable.
12 ##If the environment variable isn't set, get "", and python wrapper 9 ##If the environment variable isn't set, get "", and python wrapper
13 ##defaults to four threads. 10 ##defaults to four threads.
14 </command> 11 </command>
15 <stdio> 12 <stdio>
16 <!-- Anything other than zero is an error --> 13 <!-- Anything other than zero is an error -->
17 <exit_code range="1:" /> 14 <exit_code range="1:" />
18 <exit_code range=":-1" /> 15 <exit_code range=":-1" />
19 </stdio> 16 </stdio>
20 <inputs> 17 <inputs>
21 <param format="fasta" name="sequence" type="data" 18 <param format="fasta" name="sequence" type="data"
22 label="Input sequences for which to predict localisation (protein FASTA format)" /> 19 label="Input sequences for which to predict localisation (protein FASTA format)" />
23 <param name="type" type="select" 20 <param name="type" type="select"
24 label="Organism type (N.B. all sequences in the above file must be of the same type)" > 21 label="Organism type (N.B. all sequences in the above file must be of the same type)" >
25 <option value="-p">Gram positive bacteria</option> 22 <option value="-p">Gram positive bacteria</option>
26 <option value="-n">Gram negative bacteria</option> 23 <option value="-n">Gram negative bacteria</option>
27 <option value="-a">Archaea</option> 24 <option value="-a">Archaea</option>
28 </param> 25 </param>
29 <param name="long" type="select" label="Output type"> 26 <param name="long" type="select" label="Output type">
32 <option value="normal">Normal</option> 29 <option value="normal">Normal</option>
33 --> 30 -->
34 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option> 31 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
35 </param> 32 </param>
36 <param name="cutoff" size="10" type="float" optional="true" value="" 33 <param name="cutoff" size="10" type="float" optional="true" value=""
37 label="Sets a cutoff value for reported results (e.g. 7.5)" 34 label="Sets a cutoff value for reported results (e.g. 7.5)"
38 help="Leave blank or use zero for no cutoff." /> 35 help="Leave blank or use zero for no cutoff." />
39 <param name="divergent" size="10" type="float" optional="true" value="" 36 <param name="divergent" size="10" type="float" optional="true" value=""
40 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)" 37 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
41 help="Leave blank or use zero for no cutoff." /> 38 help="Leave blank or use zero for no cutoff." />
42 </inputs> 39 </inputs>
43 <outputs> 40 <outputs>
44 <data format="tabular" name="outfile" /> 41 <data format="tabular" name="outfile" />
45 </outputs> 42 </outputs>
46 <requirements> 43 <requirements>
100 97
101 See also http://www.psort.org/documentation/index.html 98 See also http://www.psort.org/documentation/index.html
102 99
103 This wrapper is available to install into other Galaxy Instances via the Galaxy 100 This wrapper is available to install into other Galaxy Instances via the Galaxy
104 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 101 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
102 <citations>
103 <citation type="doi">10.7717/peerj.167</citation>
104 <citation type="doi">10.1093/bioinformatics/btq249</citation>
105 </citations>
105 </help> 106 </help>
106 </tool> 107 </tool>