comparison jbrowse.xml @ 18:836d1aa3e89a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e

17:ff11d442feed

<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2">
  <description>genome browser</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command>python jbrowse.py --version</version_command>
  <command><![CDATA[

#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:

## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp $trackxml $output.files_path/galaxy.xml &&

## Once that's done, we run the python script to handle the real work
python $__tool_directory__/jbrowse.py

--jbrowse \${JBROWSE_SOURCE_DIR}
#if str($standalone) == "Complete":
    --standalone
#end if

<root>
    <metadata>
        <gencode>$gencode</gencode>
        <genomes>
            #if str($reference_genome.genome_type_select) == "indexed":
              <genome>${reference_genome.genomes.fields.path}</genome>
            #else
              #for $genome in $reference_genome.genomes:
                  <genome path="$genome">
                    <metadata>
                      <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"

                                  type="text"
                                  value=""
                                  help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
                                  optional="True"/>
                      </section>
                   </when>
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />

        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="26"/>
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================

18:836d1aa3e89a

<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
  <description>genome browser</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
  <command><![CDATA[

#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:

## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp $trackxml $output.files_path/galaxy.xml &&

## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse.py'

--jbrowse \${JBROWSE_SOURCE_DIR}
#if str($standalone) == "Complete":
    --standalone
#end if

<root>
    <metadata>
        <gencode>$gencode</gencode>
        <genomes>
            #if str($reference_genome.genome_type_select) == "indexed":
              <genome path="${reference_genome.genomes.fields.path}">
                  <metadata />
              </genome>s
            #else
              #for $genome in $reference_genome.genomes:
                  <genome path="$genome">
                    <metadata>
                      <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"

                                  type="text"
                                  value=""
                                  help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
                                  optional="True"/>
                      </section>
                  </when>
                  <when value="BlastView/View/Track/CanvasFeatures" />
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />

        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="26"/>
    </test>
    <test>
        <!-- data_table -->
        <param name="reference_genome|genome_type_select" value="indexed"/>
        <param name="reference_genome|genomes" value="merlin"/>
        <param name="gencode" value="1" />
        <param name="standalone" value="Data Directory" />
        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================