Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.xml @ 18:eb6ac44d4b8e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
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>