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comparison tools/protein_analysis/psortb.xml @ 20:a19b3ded8f33 draft

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v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
author peterjc
date Thu, 21 Sep 2017 11:35:20 -0400
parents eb6ac44d4b8e
children 238eae32483c
comparison
equal deleted inserted replaced
19:f3ecd80850e2 20:a19b3ded8f33
1 <tool id="Psortb" name="psortb" version="0.0.7"> 1 <tool id="Psortb" name="psortb" version="0.0.9">
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 <requirements> 6 <requirements>
7 <requirement type="binary">psort</requirement>
8 <requirement type="package">psort</requirement> 7 <requirement type="package">psort</requirement>
9 </requirements> 8 </requirements>
10 <stdio> 9 <version_command>
11 <!-- Anything other than zero is an error --> 10 python $__tool_directory__/psortb.py --version
12 <exit_code range="1:" /> 11 </version_command>
13 <exit_code range=":-1" /> 12 <command detect_errors="aggressive">
14 </stdio> 13 python $__tool_directory__/psortb.py "\$GALAXY_SLOTS" '$type' '$long' '$cutoff' '$divergent' '$sequence' '$outfile'
15 <version_command interpreter="python">psortb.py --version</version_command>
16 <command interpreter="python">
17 psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
18 ##If the environment variable isn't set, get "", and python wrapper
19 ##defaults to four threads.
20 </command> 14 </command>
21 <inputs> 15 <inputs>
22 <param format="fasta" name="sequence" type="data" 16 <param format="fasta" name="sequence" type="data"
23 label="Input sequences for which to predict localisation (protein FASTA format)" /> 17 label="Input sequences for which to predict localisation (protein FASTA format)" />
24 <param name="type" type="select" 18 <param name="type" type="select"