comparison jbrowse.xml @ 5:ae9382cfb6ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed

4:d022577ff9cf

<tool id="jbrowse" name="JBrowse" version="0.4">
  <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[
mkdir -p $output.files_path &&
## 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
$trackxml

--jbrowse \${JBROWSE_SOURCE_DIR}
#if str($standalone) == "Complete":
    --standalone
#end if
--outdir $output.files_path;

#if str($standalone) == "Complete":
    mv $output.files_path/index.html $output;
#else:
    mv $dummyIndex $output;

      <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
<root>
    <metadata>
        <gencode>$gencode</gencode>
        <genomes>
            #for $genome in $genomes:
                <genome>$genome</genome>
            #end for
        </genomes>
    </metadata>
    <tracks>
        #for $tg in $track_groups:
        #for $track in $tg.data_tracks:
        <track cat="${tg.category}" format="${track.data_format.data_format_select}">
            <files>
              #for $dataset in $track.data_format.annotation:
              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
              #end for
            </files>

                    <protein>${track.data_format.is_protein}</protein>
                    <min_gap>${track.data_format.min_gap}</min_gap>
                </blast>
            #else if str($track.data_format.data_format_select) == "gene_calls":
                <gff>
                  #if $track.data_format.match_part.match_part_select:
                    <match>${track.data_format.match_part.name}</match>
                  #end if
                </gff>
            #end if
            </options>
        </track>
        #end for
        #end for

</root>
]]>
      </configfile>
  </configfiles>
  <inputs>
    <param label="Fasta Sequence(s)"
           name="genomes"
           type="data"
           format="fasta"
           multiple="True"/>
    <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>

    <param label="Genetic Code" name="gencode" type="select">
      <option value="1">1. The Standard Code</option>
      <option value="2">2. The Vertebrate Mitochondrial Code</option>

                <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
                <option value="pileup">BAM Pileups</option>
                <option value="blast">Blast XML</option>
                <option value="wiggle">BigWig XY</option>
                <option value="vcf">VCF SNPs</option>
            </param>
            <when value="blast">
                <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                <param label="Features used in Blast Search"

                        description="Hit_titles"
                        height="600px"/>
                <expand macro="color_selection"
                        token_scaling_lin_select="false"
                        token_scaling_log_select="true" />
            </when>
            <when value="vcf">
                <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
            </when>
            <when value="gene_calls">
                <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
                <conditional name="match_part" label="match/match_part data">
                    <param label="This is match/match_part data"

                               help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
                               optional="False"/>
                    </when>
                    <when value="false" />
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
            </when>
            <when value="pileup">
                <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                <param label="Autogenerate SNP Track"
                       help="Not recommended for deep coverage BAM files"
                       type="boolean"
                       name="auto_snp"
                       truevalue="true"
                       falsevalue="false" />
            </when>
            <when value="wiggle">
                <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />

                <param label="Use XYPlot"

                        <param label="Track maximum" name="maximum"
                            type="integer" value="100" />
                    </when>
                </conditional>
                <expand macro="color_selection_minmax" />
            </when>
        </conditional>
    </repeat>
    </repeat>

    <param type="hidden" name="uglyTestingHack" value="" />
  </inputs>
  <outputs>
      <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
  </outputs>

=================

JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
alternative to Trackster.

The JBrowse-in-Galaxy (JiG) tool was written to help build complex
JBrowse installations straight from Galaxy, taking advantage of the
latest Galaxy features such as dataset collections, sections, and colour
pickers. It allows you to build up a JBrowse instance without worrying
about how to run the command line tools to format your data, and which

5:ae9382cfb6ac

<tool id="jbrowse" name="JBrowse" version="0.5">
  <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:
    cp -R $action.update_jbrowse.extra_files_path $output.files_path;
#end if

## 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

--outdir $output.files_path
$trackxml;

#if str($standalone) == "Complete":
    mv $output.files_path/index.html $output;
#else:
    mv $dummyIndex $output;

      <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
<root>
    <metadata>
        <gencode>$gencode</gencode>
        <genomes>
            #if str($action.genomes) != "None":
            #for $genome in $action.genomes:
                <genome>$genome</genome>
            #end for
            #end if
        </genomes>
        <general>
            <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
            <trackPadding>${jbgen.trackPadding}</trackPadding>

            <shareLink>${jbgen.shareLink}</shareLink>
            <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
            <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
            <show_nav>${jbgen.show_nav}</show_nav>
            <show_overview>${jbgen.show_overview}</show_overview>
            <show_menu>${jbgen.show_menu}</show_menu>
            <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
        </general>
    </metadata>
    <tracks>
        #for $tg in $track_groups:
        #for $track in $tg.data_tracks:
        <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
            <files>
              #for $dataset in $track.data_format.annotation:
              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
              #end for
            </files>

                    <protein>${track.data_format.is_protein}</protein>
                    <min_gap>${track.data_format.min_gap}</min_gap>
                </blast>
            #else if str($track.data_format.data_format_select) == "gene_calls":
                <gff>
                    <trackType>${track.data_format.track_class}</trackType>
                  #if $track.data_format.match_part.match_part_select:
                    <match>${track.data_format.match_part.name}</match>
                  #end if
                </gff>
##            #else if str($track.data_format.data_format_select) == "sparql":
##                <sparql>
##                    <url>${track.data_format.url}</url>
##                    <label>${track.data_format.label}</label>
##                    <!-- This is going to be an absolutey nightmare -->
##                    <query>${track.data_format.query}</query>
##                </sparql>
            #end if
            </options>
        </track>
        #end for
        #end for

</root>
]]>
      </configfile>
  </configfiles>
  <inputs>
    <conditional name="action" label="Action">
        <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
            <option value="create">New JBrowse Instance</option>
            <option value="update">Update exising JBrowse Instance</option>
        </param>
        <when value="create">
            <param label="Fasta Sequence(s)"
                   name="genomes"
                   type="data"
                   format="fasta"
                   multiple="True"/>
       </when>
        <when value="update">
            <param label="Additional Fasta Sequence(s)"
                   help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences."
                   name="genomes"
                   type="data"
                   format="fasta"
                   optional="True"
                   multiple="True"/>
            <param label="Previous JBrowse Instance"
                   name="update_jbrowse"
                   type="data"
                   format="html" />
        </when>
    </conditional>

    <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>

    <param label="Genetic Code" name="gencode" type="select">
      <option value="1">1. The Standard Code</option>
      <option value="2">2. The Vertebrate Mitochondrial Code</option>

                <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
                <option value="pileup">BAM Pileups</option>
                <option value="blast">Blast XML</option>
                <option value="wiggle">BigWig XY</option>
                <option value="vcf">VCF SNPs</option>
                <!--<option value="sparql">SPARQL</option>-->
            </param>
            <when value="blast">
                <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                <param label="Features used in Blast Search"

                        description="Hit_titles"
                        height="600px"/>
                <expand macro="color_selection"
                        token_scaling_lin_select="false"
                        token_scaling_log_select="true" />
                <expand macro="track_display" />
            </when>
            <when value="vcf">
                <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
                <expand macro="track_display" />
            </when>
            <when value="gene_calls">
                <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
                <conditional name="match_part" label="match/match_part data">
                    <param label="This is match/match_part data"

                               help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
                               optional="False"/>
                    </when>
                    <when value="false" />
                </conditional>
                <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
                  <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
                  <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
                </param>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_display" />
            </when>
            <when value="pileup">
                <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                <param label="Autogenerate SNP Track"
                       help="Not recommended for deep coverage BAM files"
                       type="boolean"
                       name="auto_snp"
                       truevalue="true"
                       falsevalue="false" />
                <expand macro="track_display" />
            </when>
            <when value="wiggle">
                <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />

                <param label="Use XYPlot"

                        <param label="Track maximum" name="maximum"
                            type="integer" value="100" />
                    </when>
                </conditional>
                <expand macro="color_selection_minmax" />
                <expand macro="track_display" />
            </when>
            <!--
            <when value="sparql">
                <param type="text" label="SPARQL Server URL" name="url" />
                <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
                <param type="text" label="SPARQL Query" name="query" area="true" />
                <expand macro="track_display" />
            </when>
            -->
        </conditional>
    </repeat>
    </repeat>

    <expand macro="general_options" />
    <param type="hidden" name="uglyTestingHack" value="" />
  </inputs>
  <outputs>
      <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
  </outputs>

=================

JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
alternative to Trackster.

Overview
--------

JBrowse is a fast, embeddable genome browser built completely with
JavaScript and HTML5.

The JBrowse-in-Galaxy (JiG) tool was written to help build complex
JBrowse installations straight from Galaxy, taking advantage of the
latest Galaxy features such as dataset collections, sections, and colour
pickers. It allows you to build up a JBrowse instance without worrying
about how to run the command line tools to format your data, and which