comparison scriptrunner.xml @ 2:495946ffc2d6 draft default tip

planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa

1:315a7e9ed6eb

<tool id="docker_scriptrunner" name="docker scriptrunner" version="1.1.6">
  <description>Runs scripts using docker</description>
  <macros>
    <import>macros.xml</import>
  </macros>
   <requirements>
      <requirement type="package" version="1.8.1">docker-py</requirement>
  </requirements>
  <command>
    python "$__tool_directory__/scriptrunner.py"
    --script_path "$runme"
    --interpreter "$interpreter"
    --user_email "$__user_email__"
    #if $generate_simple_output.make_TAB=="yes":
       --output_tab "$tab_file"
    #end if
    #if $make_HTML.value=="yes":
      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
    #else:
       --output_dir "."
    #end if
    #if $additional_parameters != 'None':
      #for i in $additional_parameters:
	--additional_parameters
        "$i.param_name, $i.param_value"
      #end for
    #end if
    #if $input_files != 'None':
       --input_tab 
	#for i in $input_files:
	  $i.input
	#end for
        #for i in $input_files:
          --input_format "Any"
        #end for
    #end if
    --docker_image "$docker_image" 
  </command>
<configfiles>
  <configfile name="runme">$dynScript</configfile>
</configfiles>
  <inputs>

         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
        <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
        <option value="" selected="true">No, no HTML output file thanks</option>
    </param>
    <conditional name="generate_simple_output">
      <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above" 
           help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
          <option value="yes" selected="true">My script writes to a new history output</option>
          <option value="">I do not want a new history output file</option>
      </param>
      <when value="yes">
        <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">

    </param>   
    <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select">
        <options from_data_table="docker_scriptrunner_images"/>
    </param>
    <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"  
      help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
      <sanitizer>
         <valid initial="string.printable">
         </valid>
         <mapping initial="none"/>
      </sanitizer>
     </param>
  </inputs>
  <outputs>
    <data format_source="input" name="tab_file">
      <filter>generate_simple_output['make_TAB'] == "yes"</filter>
        <actions>
          <action type="format">
                <option type="from_param" name="generate_simple_output.out_format" />
          </action>
        </actions>

        <filter>make_HTML == "yes"</filter>
    </data>
 </outputs>
<tests>
    <test>
        <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' />
        <param name="make_TAB" value="yes" />
        <param name="make_HTML" value="yes" />
        <param name="out_format" value="tabular" />
        <param name="interpreter" value='python' />
        <param name="runme" value="tf2_test_runme.py"/>
        <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
        <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
    </test>
</tests>
<expand macro="help_macro" />
<expand macro="test_data_macro" />
</tool>

2:495946ffc2d6

<tool id="docker_scriptrunner" name="docker scriptrunner" version="0.1.7">
  <description>Runs scripts using docker</description>
  <macros>
    <import>macros.xml</import>
  </macros>
   <requirements>
      <requirement type="package" version="3.4.1">docker-py</requirement>
  </requirements>
  <command detect_errors="exit_code">
python '$__tool_directory__/scriptrunner.py'
--script_path '$runme'
--interpreter '$interpreter'
--user_email '$__user_email__'
#if $generate_simple_output.make_file=="yes":
   --output_file "$output_file"
#end if
#if $make_HTML.value=="yes":
  --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
#else:
   --output_dir "."
#end if
#if $additional_parameters != 'None':
  #for i in $additional_parameters:
    --additional_parameters
    "$i.param_name, $i.param_value"
  #end for
#end if
#if $input_files != 'None':
   --input_file
   #for i in $input_files:
     $i.input
   #end for
   #for i in $input_files:
     --input_format "Any"
   #end for
#end if
--docker_image "$docker_image" 
  </command>
<configfiles>
  <configfile name="runme">$dynScript</configfile>
</configfiles>
  <inputs>

         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
        <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
        <option value="" selected="true">No, no HTML output file thanks</option>
    </param>
    <conditional name="generate_simple_output">
      <param name="make_file" type="select" label="Create a new history output alongside the HTML file specified above"
           help="This is useful if your script creates a single new file that you want to appear in the history after the tool executes">
          <option value="yes" selected="true">My script writes to a new history output</option>
          <option value="">I do not want a new history output file</option>
      </param>
      <when value="yes">
        <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">

    </param>   
    <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select">
        <options from_data_table="docker_scriptrunner_images"/>
    </param>
    <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"  
      help="Script must deal with two command line parameters: Path to input file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
      <sanitizer>
         <valid initial="string.printable">
         </valid>
         <mapping initial="none"/>
      </sanitizer>
     </param>
  </inputs>
  <outputs>
    <data format_source="input" name="output_file">
      <filter>generate_simple_output['make_file'] == "yes"</filter>
        <actions>
          <action type="format">
                <option type="from_param" name="generate_simple_output.out_format" />
          </action>
        </actions>

        <filter>make_HTML == "yes"</filter>
    </data>
 </outputs>
<tests>
    <test>
        <param name="input_file" value="tf2_test_in.xls" ftype="tabular"/>
        <param name="make_file" value="yes"/>
        <param name="make_HTML" value="yes"/>
        <param name="out_format" value="tabular"/>
        <param name="interpreter" value="python"/>
        <param name="runme" value="tf2_test_runme.py"/>
        <output name="output_file" file="tf2_test_out.xls" compare="diff" lines_diff="10"/>
        <output name="html_file" file="tf2_test.html" compare="diff" lines_diff="10"/>
    </test>
</tests>
<expand macro="help_macro" />
<expand macro="test_data_macro" />
</tool>