view plot_macros.xml @ 0:cb30bd36bfd0 draft default tip

planemo upload

<macros>
<token name="@plot_need_qa_headtoken@">
</token>
<xml name="plot_need_qa_outmacro">
</xml>
<token name="@plot_need_qa_token@">
'$out_folder.extra_files_path'
</token>
<xml name="plot_need_qa_macro">
    <param name="out_folder" type="data" format="tabular" label="output of qa command" />
</xml>
<token name="@plot_headtoken@">
mkdir bin_folder &amp;&amp; 
#for $k, $f in enumerate($bin_folder)
    #if $f
        ln -s "${f}" bin_folder\/${k}.fna &amp;&amp;
    #end if
#end for &amp;&amp;

mkdir plot_folder &amp;&amp; 

</token>
<xml name="plot_outmacro">
<collection name="plot_folder" type="list" label="${tool.name} on ${on_string} (plots)">
    <discover_datasets pattern="__name_and_ext__" directory="plot_folder" />
</collection>
</xml>
<token name="@plot_token@">
bin_folder
plot_folder
#if $image_type and $image_type is not None:
--image_type $image_type
#end if
#if $dpi and $dpi is not None:
--dpi $dpi
#end if
#if $font_size and $font_size is not None:
--font_size $font_size
#end if
</token>
<xml name="plot_macro">
    <param name="bin_folder" type="data" label="bins" multiple="true" format="fasta"/>
    
    <param argument="--image_type" label="desired image type" name="image_type" optional="true" type="select">
      <option value="eps">eps</option>
      <option value="pdf">pdf</option>
      <option selected="true" value="png">png</option>
      <option value="ps">ps</option>
      <option value="svg">svg</option>
    </param>
    <param argument="--dpi" label="desired DPI of output image" name="dpi" optional="true" type="integer" value="600"/>
    <param argument="--font_size" label="Desired font size" name="font_size" optional="true" type="integer" value="8"/>
</xml>
<token name="@plot_single_headtoken@">
</token>
<xml name="plot_single_outmacro">
</xml>
<token name="@plot_single_token@">
#if $width and $width is not None:
--width $width
#end if
#if $height and $height is not None:
--height $height
#end if
</token>
<xml name="plot_single_macro">
    <param argument="--width" label="width of output image" name="width" optional="true" type="float" value="6.5"/>
    <param argument="--height" label="height of output image" name="height" optional="true" type="float" value="6.5"/>
</xml>
<token name="@plot_double_headtoken@">
</token>
<xml name="plot_double_outmacro">
</xml>
<token name="@plot_double_token@">
#if $width and $width is not None:
--width $width
#end if
#if $height and $height is not None:
--height $height
#end if
</token>
<xml name="plot_double_macro">
    <param argument="--width" label="width of output image" name="width" optional="true" type="float" value="6.5"/>
    <param argument="--height" label="height of output image" name="height" optional="true" type="float" value="3.5"/>
</xml>
<token name="@plot_rows_headtoken@">
</token>
<xml name="plot_rows_outmacro">
</xml>
<token name="@plot_rows_token@">
#if $width and $width is not None:
--width $width
#end if
#if $row_height and $row_height is not None:
--row_height $row_height
#end if
</token>
<xml name="plot_rows_macro">
    <param argument="--width" label="width of output image" name="width" optional="true" type="float" value="6.5"/>
    <param argument="--row_height" label="height of each row in the output image" name="row_height" optional="true" type="float" value="0.3"/>
</xml>
</macros>