comparison toolfactory/ToolFactory.xml @ 6:efefe43f23c8 draft default tip

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5:e2c8c2fa192d

          <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
          </param>
          </repeat>
      </xml>
     <xml name="tool_metadata">
         <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
            <param name="tool_desc" label="Tool Synopsis" type="text" value=""
             help="Supply a brief tool description for the Galaxy tool menu entry" />
             <param name="install" label="Attempt to install in the host Galaxy"
                help="This will fail unless running in a very unusual configuration such as a specialised Docker container"
                type="boolean" checked="True" truevalue="1"  falsevalue="0" />
         <conditional name="do_test">
            <param name="run_test" label="Run planemo test on the new archive to add test outputs making a proper tool - takes time"
                help="Archives must be run and updated using planemo to populate all the test outputs. Will be very quick if no dependencies (eg a bash script). May take a very long time depending on dependencies"
                type="boolean" checked="False" truevalue="1"  falsevalue="0" />
                <when value="0">
                    <param name="tail" type="hidden" value="not_tested"/>
                </when>
                <when value="1">
                    <param name="tail" type="hidden" value="tested"/>
                </when>
            </conditional>
            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
            value="**What it Does**"
             help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
                <sanitizer>
                    <valid initial="string.printable" />

--help_text "$helpme"
--new_tool "$new_tool"
    #if $install:
       --install
    #end if
    #if $do_test.run_test:
       --run_test
    #end if
   #if $io_param.ppass.parampass != '0':
     #if str($io_param.ppass.addparam.edit_params) == "yes":
--edit_additional_parameters

        </when>
    </conditional>
    <expand macro="tool_metadata" />
  </inputs>
  <outputs>
    <data format="toolshed.gz" name="new_tool" label="${tool_name}_${do_test.tail}_toolshed.gz" />
   <collection name="TF_run_report" type="list" label="${tool_name} test run outputs">
      <filter>do_test['run_test']</filter>
      <discover_datasets pattern="__name_and_ext__" directory="TF_run_report" />
  </collection>
  </outputs>
<tests>
<test>
    <param name="user_email" value="[e-mail]"/>
    <param name="input_files" value="input1_sample" />

    <param name="history_CL" value="2" />
    <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
    <param name="choosescript" value="yes" />
    <param name="script_path" value="$runme"/>
    <param name="install" value="0"/>
    <param name="run_test" value="1"/>
    <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
</test>
</tests>
<help>

6:efefe43f23c8

          <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
          </param>
          </repeat>
      </xml>
     <xml name="tool_metadata">
        <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
        <param name="tool_desc" label="Tool Synopsis" type="text" value=""
            help="Supply a brief tool description for the Galaxy tool menu entry" />
        <param name="install" label="Attempt to install in the host Galaxy"
            help="This will fail unless running in a very unusual configuration such as a specialised Docker container"
            type="boolean" checked="False" truevalue="1"  falsevalue="0" />
         <param name="run_test" label="Finalise new archive with test outputs. Runs externally. Outputs will appear in history when ready"
                    help="Archives must be run and updated using planemo to populate all the test outputs. May take a long time depending on dependencies"
                    type="boolean" checked="True" truevalue="1"  falsevalue="0" />
            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
            value="**What it Does**"
             help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
                <sanitizer>
                    <valid initial="string.printable" />

--help_text "$helpme"
--new_tool "$new_tool"
    #if $install:
       --install
    #end if
    #if $run_test:
       --run_test
    #end if
   #if $io_param.ppass.parampass != '0':
     #if str($io_param.ppass.addparam.edit_params) == "yes":
--edit_additional_parameters

        </when>
    </conditional>
    <expand macro="tool_metadata" />
  </inputs>
  <outputs>
    <data format="toolshed.gz" name="new_tool" label="${tool_name}_not_tested.toolshed.gz" />
  </outputs>
<tests>
<test>
    <param name="user_email" value="[e-mail]"/>
    <param name="input_files" value="input1_sample" />

    <param name="history_CL" value="2" />
    <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
    <param name="choosescript" value="yes" />
    <param name="script_path" value="$runme"/>
    <param name="install" value="0"/>
    <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
</test>
</tests>
<help>