Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/promoter2.xml @ 26:20139cb4c844 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
author peterjc
date Wed, 13 May 2015 06:14:42 -0400
parents 41a42022f815
children 22e71e53f534
comparison
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25:41a42022f815 26:20139cb4c844
1 <tool id="promoter2" name="Promoter 2.0" version="0.0.8"> 1 <tool id="promoter2" name="Promoter 2.0" version="0.0.9">
2 <description>Find eukaryotic PolII promoters in DNA sequences</description> 2 <description>Find eukaryotic PolII promoters in DNA 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 per chunk so 4 threads each doing 500 is ideal --> 4 <!-- Using 2000 per chunk so 4 threads each doing 500 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">promoter</requirement>
8 <requirement type="package">promoter</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 promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file" 16 promoter2.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 DNA sequences"/> 21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/>
18 </inputs> 22 </inputs>
19 <outputs> 23 <outputs>
20 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" /> 24 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />
21 </outputs> 25 </outputs>
22 <requirements>
23 <requirement type="binary">promoter</requirement>
24 </requirements>
25 <tests> 26 <tests>
26 <test> 27 <test>
27 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/> 28 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>
28 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/> 29 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/>
29 </test> 30 </test>