comparison gmap_build.xml @ 5:14561eb803a5 draft

Uploaded v3.0.1b (still working on this prior to main Tool Shed release)

4:a88571642c6e

  <description>a database genome index for GMAP and GSNAP</description>
  <requirements>
      <requirement type="package" version="2013-05-09">gmap</requirement>
  </requirements>
  <version_command>gmap --version</version_command>
  <command interpreter="command"> /bin/bash $shscript > $output </command>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash
#set $ds = chr(36)
#set $gt = chr(62)

      <option value="13">13 (256MB RAM)</option>
      <option value="14">14 (1GB RAM)</option>
      <option value="15" selected="true">15 (4GB RAM)</option>
    </param>
  </inputs>
  <stdio>
    <exit_code range="1"  level="fatal"   description="Error running gmap_build" />
  </stdio>
  <outputs>
    <!--
    <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
    -->
    <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />

5:14561eb803a5

  <description>a database genome index for GMAP and GSNAP</description>
  <requirements>
      <requirement type="package" version="2013-05-09">gmap</requirement>
  </requirements>
  <version_command>gmap --version</version_command>
  <command detect_errors="exit_code"><![CDATA[
/bin/bash $shscript > $output
  ]]></command>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash
#set $ds = chr(36)
#set $gt = chr(62)

      <option value="13">13 (256MB RAM)</option>
      <option value="14">14 (1GB RAM)</option>
      <option value="15" selected="true">15 (4GB RAM)</option>
    </param>
  </inputs>
  <outputs>
    <!--
    <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
    -->
    <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />