Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/promoter2.xml @ 18:eb6ac44d4b8e draft
Suite v0.2.8, record Promoter 2 verion + misc internal updates
author | peterjc |
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date | Tue, 01 Sep 2015 09:56:36 -0400 |
parents | e6cc27d182a8 |
children | a19b3ded8f33 |
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17:e6cc27d182a8 | 18:eb6ac44d4b8e |
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1 <tool id="promoter2" name="Promoter 2.0" version="0.0.8"> | 1 <tool id="promoter2" name="Promoter 2.0" version="0.0.10"> |
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> | |
15 <version_command interpreter="python">promoter2.py --version</version_command> | |
6 <command interpreter="python"> | 16 <command interpreter="python"> |
7 promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file" | 17 promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file" |
8 ##If the environment variable isn't set, get "", and the python wrapper | 18 ##If the environment variable isn't set, get "", and the python wrapper |
9 ##defaults to four threads. | 19 ##defaults to four threads. |
10 </command> | 20 </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> | 21 <inputs> |
17 <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/> | 22 <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/> |
18 </inputs> | 23 </inputs> |
19 <outputs> | 24 <outputs> |
20 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" /> | 25 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" /> |
21 </outputs> | 26 </outputs> |
22 <requirements> | |
23 <requirement type="binary">promoter</requirement> | |
24 </requirements> | |
25 <tests> | 27 <tests> |
26 <test> | 28 <test> |
27 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/> | 29 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/> |
28 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/> | 30 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/> |
29 </test> | 31 </test> |