Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/tmhmm2.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="tmhmm2" name="TMHMM 2.0" version="0.0.13"> | 1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.14"> |
| 2 <description>Find transmembrane domains in protein sequences</description> | 2 <description>Find transmembrane domains in 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 <requirements> | |
| 7 <requirement type="binary">tmhmm</requirement> | |
| 8 <requirement type="package">tmhmm</requirement> | |
| 9 </requirements> | |
| 10 <stdio> | |
| 11 <!-- Anything other than zero is an error --> | |
| 12 <exit_code range="1:" /> | |
| 13 <exit_code range=":-1" /> | |
| 14 </stdio> | |
| 6 <command interpreter="python"> | 15 <command interpreter="python"> |
| 7 tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file | 16 tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file |
| 8 ##If the environment variable isn't set, get "", and the python wrapper | 17 ##If the environment variable isn't set, get "", and the python wrapper |
| 9 ##defaults to four threads. | 18 ##defaults to four threads. |
| 10 </command> | 19 </command> |
| 11 <stdio> | |
| 12 <!-- Anything other than zero is an error --> | |
| 13 <exit_code range="1:" /> | |
| 14 <exit_code range=":-1" /> | |
| 15 </stdio> | |
| 16 <inputs> | 20 <inputs> |
| 17 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> | 21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> |
| 18 <!-- | 22 <!-- |
| 19 <param name="version" type="select" display="radio" label="Model version"> | 23 <param name="version" type="select" display="radio" label="Model version"> |
| 20 <option value="">Version 1 (old)</option> | 24 <option value="">Version 1 (old)</option> |
| 23 --> | 27 --> |
| 24 </inputs> | 28 </inputs> |
| 25 <outputs> | 29 <outputs> |
| 26 <data name="tabular_file" format="tabular" label="TMHMM results" /> | 30 <data name="tabular_file" format="tabular" label="TMHMM results" /> |
| 27 </outputs> | 31 </outputs> |
| 28 <requirements> | |
| 29 <requirement type="binary">tmhmm</requirement> | |
| 30 </requirements> | |
| 31 <tests> | 32 <tests> |
| 32 <test> | 33 <test> |
| 33 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> | 34 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> |
| 34 <output name="tabular_file" file="four_human_proteins.tmhmm2.tabular" ftype="tabular"/> | 35 <output name="tabular_file" file="four_human_proteins.tmhmm2.tabular" ftype="tabular"/> |
| 35 </test> | 36 </test> |