comparison rgToolFactory.xml @ 30:fb3fa6a2874d draft

Citations added (thanks John!) and a few more output formats for Alistair Chilcott

29:bff4c9bfabc7

<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="1.3.18">graphicsmagick</requirement>
  </requirements>
  <command interpreter="python">

      --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 "."

            <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="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>

        <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>

<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>

30:fb3fa6a2874d

<tool id="rgTF" name="Tool Factory" version="1.11">
  <description>Run a script; make a tool!</description>
   <requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.18">graphicsmagick</requirement>
  </requirements>
  <command interpreter="python">

      --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 "."

            <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="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>
    <option value="sam">sam</option>
    <option value="bam">bam</option>
    <option value="fastqsanger">fastqsanger</option>
    <option value="fastq">fastq</option>
    <option value="fasta">fasta</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="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>

        <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"  />
            <when input="out_format" value="sam" format="sam" />
            <when input="out_format" value="bam"  format=bam"  />
            <when input="out_format" value="fastqsanger" format="fastqsanger" />
            <when input="out_format" value="fastq"  format=fastq"  />
         </change_format>
    </data>
    <data format="html" name="html_file" label="${tool_name}.html">
        <filter>make_HTML == "yes"</filter>
    </data>

<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>