comparison rgToolFactory.xml @ 43:c5bfdb0f7041 draft

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42:4b807bc775ad

<tool id="rgTF" name="Tool Factory" version="1.10">
  <description>Makes scripts into tools</description>
   <requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.18">graphicsmagick</requirement>
  </requirements>
  <command interpreter="python">
#if ( $__user_email__ not in $__admin_users__ ):
     rgToolFactory.py --bad_user $__user_email__
#else:
    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
     --tool_name "$tool_name"  --user_email "$__user_email__"
    #if $make_TAB.value=="yes":
       --output_tab "$tab_file"
    #end if
    #if $makeMode.make_Tool=="yes":
      --make_Tool "$makeMode.make_Tool"
      --tool_desc "$makeMode.tool_desc"
      --tool_version "$makeMode.tool_version"
      --new_tool "$new_tool"
      --help_text "$helpme"
      #if $make_HTML.value=="yes":
      --include_dependencies "${makeMode.include_deps}"
      #end if
    #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 $input1 != 'None':
       --input_tab "$input1"
    #end if
#end if 
  </command>
  <inputs>
    <param name="input1"  type="data"  label="Select an input file from your history" optional="true" size="120"
       help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
    <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
         help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits"/>
        </sanitizer>

            <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
            help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
                <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
                <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
            </param>

        </when>
        <when value = "">
        </when>
    </conditional> 
    <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"

    <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an 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>
    <param name="out_format" type="select" label="Galaxy datatype for your tool's output file if any" help="You may need to edit the xml to extend this list">
    <option value="tabular" selected="true">Tabular</option>
    <option value="interval">Interval</option>
    <option value="gz">gz</option>
    <option value="text">text</option>
    </param>
    <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
        <option value="Rscript" selected="true">Rscript</option>
        <option value="python">python</option>
        <option value="perl">perl</option>
        <option value="sh">sh</option>
    </param>   
    <param name="dynScript" label="Cut 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>

         <mapping initial="none"/>
      </sanitizer>
     </param>
  </inputs>
  <outputs>
    <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
        <filter>make_TAB=="yes"</filter>
        <change_format>
            <when input="out_format" value="interval"  format="interval" />
            <when input="out_format" value="gz" format="gz" />
            <when input="out_format" value="text"  format="text"  />
         </change_format>
    </data>
    <data format="html" name="html_file" label="${tool_name}.html">
        <filter>make_HTML == "yes"</filter>
    </data>
    <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">

<configfiles>
<configfile name="runme">$dynScript</configfile>
<configfile name="helpme">
#if $makeMode.make_Tool == "yes":
${makeMode.help_text}
#end if
</configfile>
</configfiles>
<help>
    

.. _GTFI:  https://bitbucket.org/fubar/galaxytoolfactory/issues
.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref


</help>

</tool>

43:c5bfdb0f7041

<tool id="rgTF" name="Tool Factory" version="1.11">
  <description>Makes scripts into tools</description>
   <requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.20">graphicsmagick</requirement>
  </requirements>
  <command interpreter="python">
#if ( $__user_email__ not in $__admin_users__ ):
     rgToolFactory.py --bad_user $__user_email__
#else:
    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
     --tool_name "$tool_name"  --user_email "$__user_email__"
    #if $make_TAB.value=="yes":
       --output_tab "$tab_file"
       --output_format "$output_format"
    #end if
    #if $makeMode.make_Tool=="yes":
      --make_Tool "$makeMode.make_Tool"
      --tool_desc "$makeMode.tool_desc"
      --tool_version "$makeMode.tool_version"
      --new_tool "$new_tool"
      --help_text "$helpme"
      #if $make_HTML.value=="yes":
          #if makeMode.include_deps.value=="yes":
             --include_dependencies "yes"
          #end if
      #end if
      --citations "$citeme"
    #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 $input1 != 'None':
       --input_tab "$input1"
       --input_formats "$input_formats"
    #end if
#end if 
  </command>
  <inputs>
    <param name="input1"  type="data"  label="Select an input file from your history" optional="true" size="120"
       help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
    <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
    help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
     <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
        <column name="value" index="0"/>
     </options>
    </param>
    <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
         help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits"/>
        </sanitizer>

            <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
            help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
                <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
                <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
            </param>
            <repeat name="citations" title="Citation">
                <conditional name="citation_type">
                    <param name="type" type="select" label="Citation Type">
                        <option value="doi">DOI</option>
                        <option value="bibtex">BibTeX</option>
                    </param>
                    <when value="doi">
                        <param name="doi" label="DOI" type="text" value="" 
                        help="Supply a DOI (e.g. 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
                    </when>
                    <when value="bibtex">
                        <param name="bibtex" label="BibTex" type="text" area="true" size="8x120"
                            help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
                            <sanitizer>
                                <valid initial="string.printable">
                                </valid>
                                <mapping initial="none"/>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value = "">
        </when>
    </conditional> 
    <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"

    <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an 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>
   <param name="output_format" type="select" label="Select the datatype for the file your tool/script will write"
     help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
     <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
        <column name="value" index="0"/>
     </options>
    </param>
    <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
        <option value="Rscript" selected="true">Rscript</option>
        <option value="python">python</option>
        <option value="perl">perl</option>
        <option value="bash">bash</option>
        <option value="sh">sh</option>
    </param>   
    <param name="dynScript" label="Cut 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>

         <mapping initial="none"/>
      </sanitizer>
     </param>
  </inputs>
  <outputs>
    <data format="input" name="tab_file" label="${tool_name}.${output_format}">
      <filter>make_TAB == "yes"</filter>
        <actions>
          <action type="format">
                <option type="from_param" name="output_format" />
          </action>
        </actions>
    </data>
    <data format="html" name="html_file" label="${tool_name}.html">
        <filter>make_HTML == "yes"</filter>
    </data>
    <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">

<configfiles>
<configfile name="runme">$dynScript</configfile>
<configfile name="helpme">
#if $makeMode.make_Tool == "yes":
${makeMode.help_text}
#end if
</configfile>
<configfile name="citeme">
#if $makeMode.make_Tool == "yes":
#for $citation in $makeMode.citations:
#if $citation.citation_type.type == "bibtex":
**ENTRY**bibtex
${citation.citation_type.bibtex}
#else
**ENTRY**doi
${citation.citation_type.doi}
#end if
#end for
#end if
</configfile>
</configfiles>
<help>
    

.. _GTFI:  https://bitbucket.org/fubar/galaxytoolfactory/issues
.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref


</help>
<citations>
    <citation type="doi">10.1093/bioinformatics/bts573</citation>
</citations>
</tool>