comparison macros.xml @ 17:ff11d442feed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

16:b5c5470d7c09

      <requirement type="package" version="3.11">pyyaml</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
  <token name="@WRAPPER_VERSION@">0.5.3</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"

    <param type="select" label="Track Visibility" name="track_visibility">
      <option value="default_off">Off for new users</option>
      <option value="default_on">On for new users</option>
      <option value="force">Force On</option>
      <option value="always">Always On (ignores URL parameters)</option>
    </param>
  </xml>

  <xml name="jb_color"
      token_label="JBrowse style.color"

        </when>
        <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">
              <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">

      </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@"
               help="Set CSS style.className property"/>

        <param label="JBrowse style.height"
               type="text"
               name="style_height"
               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">

17:ff11d442feed

      <requirement type="package" version="3.11">pyyaml</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
  <token name="@WRAPPER_VERSION@">0.7.0</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"

    <param type="select" label="Track Visibility" name="track_visibility">
      <option value="default_off">Off for new users</option>
      <option value="default_on">On for new users</option>
      <option value="force">Force On</option>
      <option value="always">Always On (ignores URL parameters)</option>
    </param>
    <param type="select" label="Override Apollo Plugins" name="override_apollo_plugins" help="Disable the apollo plugin for this track, this disables the ability to make an annotation from this feature.">
      <option value="True">Yes - Override</option>
      <option value="False" selected="True">No - Do not Override</option>
    </param>
    <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality.">
      <option value="True">Yes - Override</option>
      <option value="False" selected="True">No - Do not Override</option>
    </param>
  </xml>

  <xml name="jb_color"
      token_label="JBrowse style.color"

        </when>
        <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="false">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">
              <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">

      </conditional>
    </section>
  </xml>
  <xml name="track_styling"
       token_classname="feature"
       token_label="product,name,id"
       token_description="note,description"
       token_height="10px"
       token_maxheight="600">
    <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
        <param label="JBrowse style.className" type="text"
               name="style_classname"
               value="@CLASSNAME@"
               help="Set CSS style.className property"/>

        <param label="JBrowse style.height"
               type="text"
               name="style_height"
               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."/>
        <param label="JBrowse maxHeight"
               type="text"
               name="max_height"
               value="@MAXHEIGHT@"
               help="Maximum height that the track is permitted to reach in pixels."/>
    </section>
  </xml>

  <xml name="track_menu">
    <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">