comparison tools/protein_analysis/psortb.xml @ 19:4cd848c5590b draft

Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.

18:2b35b5c4b7f4

<tool id="Psortb" name="psortb" version="0.0.2">
  <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
  <!-- If job splitting is enabled, break up the query file into parts -->
  <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
  <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
  <version_command interpreter="python">psortb.py --version</version_command>
  <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />
  </stdio>

19:4cd848c5590b

<tool id="Psortb" name="psortb" version="0.0.3">
  <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
  <!-- If job splitting is enabled, break up the query file into parts -->
  <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
  <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
  <version_command interpreter="python">psortb.py --version</version_command>
  <command interpreter="python">
    psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
    ##I want the number of threads to be a Galaxy config option...
    ##Set the number of threads in the runner entry in universe_wsgi.ini
    ##which (on SGE at least) will set the $NSLOTS environment variable.
    ##If the environment variable isn't set, get "", and python wrapper
    ##defaults to four threads.
  </command>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />
  </stdio>