Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/psortb.xml @ 18:eb6ac44d4b8e draft
Suite v0.2.8, record Promoter 2 verion + misc internal updates
| author | peterjc |
|---|---|
| date | Tue, 01 Sep 2015 09:56:36 -0400 |
| parents | e6cc27d182a8 |
| children | a19b3ded8f33 |
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| 17:e6cc27d182a8 | 18:eb6ac44d4b8e |
|---|---|
| 1 <tool id="Psortb" name="psortb" version="0.0.5"> | 1 <tool id="Psortb" name="psortb" version="0.0.7"> |
| 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 <requirements> |
| 7 <command interpreter="python"> | 7 <requirement type="binary">psort</requirement> |
| 8 psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile" | 8 <requirement type="package">psort</requirement> |
| 9 ##If the environment variable isn't set, get "", and python wrapper | 9 </requirements> |
| 10 ##defaults to four threads. | 10 <stdio> |
| 11 </command> | 11 <!-- Anything other than zero is an error --> |
| 12 <stdio> | 12 <exit_code range="1:" /> |
| 13 <!-- Anything other than zero is an error --> | 13 <exit_code range=":-1" /> |
| 14 <exit_code range="1:" /> | 14 </stdio> |
| 15 <exit_code range=":-1" /> | 15 <version_command interpreter="python">psortb.py --version</version_command> |
| 16 </stdio> | 16 <command interpreter="python"> |
| 17 <inputs> | 17 psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile" |
| 18 <param format="fasta" name="sequence" type="data" | 18 ##If the environment variable isn't set, get "", and python wrapper |
| 19 label="Input sequences for which to predict localisation (protein FASTA format)" /> | 19 ##defaults to four threads. |
| 20 <param name="type" type="select" | 20 </command> |
| 21 label="Organism type (N.B. all sequences in the above file must be of the same type)" > | 21 <inputs> |
| 22 <option value="-p">Gram positive bacteria</option> | 22 <param format="fasta" name="sequence" type="data" |
| 23 <option value="-n">Gram negative bacteria</option> | 23 label="Input sequences for which to predict localisation (protein FASTA format)" /> |
| 24 <option value="-a">Archaea</option> | 24 <param name="type" type="select" |
| 25 </param> | 25 label="Organism type (N.B. all sequences in the above file must be of the same type)" > |
| 26 <param name="long" type="select" label="Output type"> | 26 <option value="-p">Gram positive bacteria</option> |
| 27 <option value="terse">Short (terse, tabular with 3 columns)</option> | 27 <option value="-n">Gram negative bacteria</option> |
| 28 <!-- The normal output is text, not tabular - worth offering? | 28 <option value="-a">Archaea</option> |
| 29 <option value="normal">Normal</option> | 29 </param> |
| 30 --> | 30 <param name="long" type="select" label="Output type"> |
| 31 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option> | 31 <option value="terse">Short (terse, tabular with 3 columns)</option> |
| 32 </param> | 32 <!-- The normal output is text, not tabular - worth offering? |
| 33 <param name="cutoff" size="10" type="float" optional="true" value="" | 33 <option value="normal">Normal</option> |
| 34 label="Sets a cutoff value for reported results (e.g. 7.5)" | 34 --> |
| 35 help="Leave blank or use zero for no cutoff." /> | 35 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option> |
| 36 <param name="divergent" size="10" type="float" optional="true" value="" | 36 </param> |
| 37 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)" | 37 <param name="cutoff" size="10" type="float" optional="true" value="" |
| 38 help="Leave blank or use zero for no cutoff." /> | 38 label="Sets a cutoff value for reported results (e.g. 7.5)" |
| 39 </inputs> | 39 help="Leave blank or use zero for no cutoff." /> |
| 40 <outputs> | 40 <param name="divergent" size="10" type="float" optional="true" value="" |
| 41 <data format="tabular" name="outfile" /> | 41 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)" |
| 42 </outputs> | 42 help="Leave blank or use zero for no cutoff." /> |
| 43 <requirements> | 43 </inputs> |
| 44 <requirement type="binary">psort</requirement> | 44 <outputs> |
| 45 </requirements> | 45 <data format="tabular" name="outfile" /> |
| 46 <tests> | 46 </outputs> |
| 47 <test> | 47 <tests> |
| 48 <param name="sequence" value="empty.fasta" ftype="fasta"/> | 48 <test> |
| 49 <param name="long" value="terse"/> | 49 <param name="sequence" value="empty.fasta" ftype="fasta"/> |
| 50 <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/> | 50 <param name="long" value="terse"/> |
| 51 </test> | 51 <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/> |
| 52 <test> | 52 </test> |
| 53 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/> | 53 <test> |
| 54 <param name="long" value="terse"/> | 54 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/> |
| 55 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/> | 55 <param name="long" value="terse"/> |
| 56 </test> | 56 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/> |
| 57 </tests> | 57 </test> |
| 58 <help> | 58 </tests> |
| 59 <help> | |
| 59 | 60 |
| 60 **What it does** | 61 **What it does** |
| 61 | 62 |
| 62 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic | 63 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic |
| 63 localization sites. The input dataset needs to be protein FASTA sequences. | 64 localization sites. The input dataset needs to be protein FASTA sequences. |
| 97 | 98 |
| 98 See also http://www.psort.org/documentation/index.html | 99 See also http://www.psort.org/documentation/index.html |
| 99 | 100 |
| 100 This wrapper is available to install into other Galaxy Instances via the Galaxy | 101 This wrapper is available to install into other Galaxy Instances via the Galaxy |
| 101 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | 102 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
| 103 </help> | |
| 102 <citations> | 104 <citations> |
| 103 <citation type="doi">10.7717/peerj.167</citation> | 105 <citation type="doi">10.7717/peerj.167</citation> |
| 104 <citation type="doi">10.1093/bioinformatics/btq249</citation> | 106 <citation type="doi">10.1093/bioinformatics/btq249</citation> |
| 105 </citations> | 107 </citations> |
| 106 </help> | |
| 107 </tool> | 108 </tool> |