comparison macros.xml @ 8:ad4b9d7eae6a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9

7:1e74f16adaa1

<?xml version="1.0"?>
<macros>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.12.0">jbrowse</requirement>
      <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
      <requirement type="package" version="2.7">python</requirement>
      <requirement type="package" version="5.18.1">perl</requirement>
      <requirement type="package" version="1.66">biopython</requirement>
      <requirement type="package" version="0.6.2">bcbiogff</requirement>
      <requirement type="package" version="1.2">samtools</requirement>
      <requirement type="package" version="3.11">pyyaml</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@WRAPPER_VERSION@">1.0</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:"/>
      <exit_code range=":-1"/>
      <regex match="Error:"/>

**Attribution**

This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
]]>
  </token>
  
  <xml name="genome_selector"
    token_help=""
    token_label="Fasta sequences"
    token_optional="False" >
    <conditional name="reference_genome">
        <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
            <option selected="True" value="indexed">Use a built-in genome</option>
            <option value="history">Use a genome from history</option>
        </param>
        <when value="indexed">
            <param 
              help="@HELP@"
              label="@LABEL@"
              name="genomes"
              type="select"
              optional="@OPTIONAL@"
              >
                <options from_data_table="all_fasta">
                    <filter column="2" type="sort_by" />
                    <validator message="No genomes are available for the selected input dataset" type="no_options" />
                </options>
            </param>
        </when>
        <when value="history">
            <param 
              format="fasta"
              label="@LABEL@"
              help="@HELP@"
              name="genomes"
              type="data"
              optional="@OPTIONAL@"
              multiple="True" />
        </when>
    </conditional>
  </xml>
  
  <xml name="auto_manual_tk"
      token_cond_label="Color"
      token_cond_name="color"
      token_select_label="Color Specification"
      token_select_name="color_select"

        <when value="score">
            <!-- Scaling -->
            <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
                   help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
              <option value="linear"      selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
              <option value="logarithmic" selected=""                     >Logarithmic scaling</option>
              <option value="blast"       selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
            </param>

            <!-- Scaling Bounds -->
            <conditional name="score_scales" label="Minimum/Maximum values for track scores">

      </conditional>
    </section>
  </xml>
  <xml name="track_styling"
       token_classname="feature"
       token_label="prodcut,name,id"
       token_description="note"
       token_height="100px">
    <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
        <param label="JBrowse style.className" type="text"
               name="style_classname"
               value="@CLASSNAME@"

               value="@HEIGHT@"
               help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
    </section>
  </xml>

  <xml name="input_conditional" token_label="Track Data" token_format="data">
      <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
  </xml>
</macros>

8:ad4b9d7eae6a

<?xml version="1.0"?>
<macros>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.12.1">jbrowse</requirement>
      <requirement type="package" version="2.7">python</requirement>
      <requirement type="package" version="1.66">biopython</requirement>
      <requirement type="package" version="0.6.2">bcbiogff</requirement>
      <requirement type="package" version="1.2">samtools</requirement>
      <requirement type="package" version="3.11">pyyaml</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
  <token name="@WRAPPER_VERSION@">0.5.1</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:"/>
      <exit_code range=":-1"/>
      <regex match="Error:"/>

**Attribution**

This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
]]>
  </token>
  <xml name="auto_manual_tk"
      token_cond_label="Color"
      token_cond_name="color"
      token_select_label="Color Specification"
      token_select_name="color_select"

        <when value="score">
            <!-- Scaling -->
            <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
                   help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
              <option value="linear"      selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
              <option value="logarithmic">Logarithmic scaling</option>
              <option value="blast"       selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
            </param>

            <!-- Scaling Bounds -->
            <conditional name="score_scales" label="Minimum/Maximum values for track scores">

      </conditional>
    </section>
  </xml>
  <xml name="track_styling"
       token_classname="feature"
       token_label="name,id"
       token_description="note,description"
       token_height="100px">
    <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
        <param label="JBrowse style.className" type="text"
               name="style_classname"
               value="@CLASSNAME@"

               value="@HEIGHT@"
               help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
    </section>
  </xml>

  <xml name="track_menu">
    <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
      <repeat name="track_menu" title="Track Menu">
          <param label="Menu action"
                 type="select"
                 name="menu_action"
                 help="Action performed when user clicks on the menu">
            <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
            <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
            <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
          </param>
          <param label="Menu label"
                 type="text"
                 name="menu_label"
                 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
           <expand macro="menu_sanitize" />
          </param>
          <param label="Menu title"
                 type="text"
                 name="menu_title"
                 help="Will be displayed in the popup title bar if displayed ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
           <expand macro="menu_sanitize" />
          </param>
          <param label="Menu url"
                 type="text"
                 name="menu_url"
                 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
           <expand macro="menu_sanitize" />
          </param>
          <param label="Menu icon"
                 type="select"
                 name="menu_icon"
                 help="Icon to display next to menu label">
            <option value="dijitIconBookmark" selected="true">Bookmark</option>
            <option value="dijitIconSave">Save</option>
            <option value="dijitIconPrint">Print</option>
            <option value="dijitIconCut">Cut</option>
            <option value="dijitIconCopy">Copy</option>
            <option value="dijitIconClear">Clear</option>
            <option value="dijitIconDelete">Delete</option>
            <option value="dijitIconUndo">Undo</option>
            <option value="dijitIconEdit">Edit</option>
            <option value="dijitIconNewTask">New Task</option>
            <option value="dijitIconEditTask">Edit Task</option>
            <option value="dijitIconEditProperty">Edit Property</option>
            <option value="dijitIconTask">Task</option>
            <option value="dijitIconFilter">Filter</option>
            <option value="dijitIconConfigure">Configure</option>
            <option value="dijitIconSearch">Search</option>
            <option value="dijitIconApplication">Application</option>
            <option value="dijitIconChart">Chart</option>
            <option value="dijitIconConnector">Connector</option>
            <option value="dijitIconDatabase">Database</option>
            <option value="dijitIconDocuments">Documents</option>
            <option value="dijitIconMail">Mail</option>
            <option value="dijitLeaf">Leaf</option>
            <option value="dijitIconFile">File</option>
            <option value="dijitIconFunction">Function</option>
            <option value="dijitIconKey">Key</option>
            <option value="dijitIconPackage">Package</option>
            <option value="dijitIconSample">Sample</option>
            <option value="dijitIconTable">Table</option>
            <option value="dijitIconUsers">Users</option>
            <option value="dijitIconFolderClosed">Folder Closed</option>
            <option value="dijitIconFolderOpen">Folder Open</option>
            <option value="dijitIconError">Error</option>
          </param>
      </repeat>
    </section>
  </xml>

  <xml name="menu_sanitize">
    <sanitizer>
        <valid>
            <add value="{"/>
            <add value="}"/>
            <add value="!"/>
            <add value="?"/>
            <add value="&amp;"/>
            <add value="+"/>
            <add value="="/>
            <add value="'"/>
            <add value='"'/>
        </valid>
    </sanitizer>
  </xml>

  <xml name="input_conditional" token_label="Track Data" token_format="data">
      <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
  </xml>
  <xml name="citations">
    <citations>
      <citation type="doi">10.1101/gr.094607.109</citation>
    </citations>
  </xml>
</macros>