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Addition of Genome fasta file loading in local IGV instance, and addition of fai format and fasta to fai converter
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Delphine-L
@@ -62,12 +62,16 @@
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<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
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<datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="True" display_in_upload="False"/>
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<datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
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<datatype extension="fai" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="True" description="A Fasta Index File is a text file consisting of lines each with five TAB-delimited columns : Name, Length, offset, linebases, Linewidth" description_url="http://www.htslib.org/doc/faidx.html">
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</datatype>
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<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta">
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<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
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<converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
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<converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
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<converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
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<converter file="fasta_to_len.xml" target_datatype="len"/>
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<converter file="fasta_to_fai.xml" target_datatype="fai"/>
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<display file="igv/genome_fasta.xml" inherit="True"/>
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</datatype>
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<datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq">
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<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
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@@ -0,0 +1,92 @@
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<?xml version="1.0"?>
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<display id="igv_fasta" version="1.0.0" name="display with IGV">
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<!-- Load links from file: one line to one link -->
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<dynamic_links site_type="igv" skip_startswith="#" id="0" name="1">
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<!-- Define parameters by column from file, allow splitting on builds -->
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<dynamic_param name="site_id" value="0"/>
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<dynamic_param name="site_name" value="1"/>
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<dynamic_param name="site_link" value="2"/>
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<dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
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<dynamic_param name="site_organisms" value="4" split="True" separator="," />
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<!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
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<filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
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<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
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<url>${redirect_url}</url>
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<param type="data" name="fasta_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
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<param type="template" name="site_organism" strip="True" >
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#if ($dataset.dbkey in $site_dbkeys)
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$site_organisms[ $site_dbkeys.index( $fasta_file.dbkey ) ]
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#else:
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$fasta_file.dbkey
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#end if
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</param>
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<param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
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<?xml version="1.0" encoding="utf-8"?>
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<jnlp
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spec="1.0+"
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codebase="${site_link}">
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<information>
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<title>IGV 1.5</title>
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<vendor>The Broad Institute</vendor>
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<homepage href="http://www.broadinstitute.org/igv"/>
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<description>IGV Software</description>
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<description kind="short">IGV</description>
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</information>
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<security>
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<all-permissions/>
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</security>
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<resources>
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<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/>
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<jar href="igv.jar" download="eager" main="true"/>
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<jar href="batik-codec.jar" download="eager"/>
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<property name="apple.laf.useScreenMenuBar" value="true"/>
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<property name="com.apple.mrj.application.growbox.intrudes" value="false"/>
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<property name="com.apple.mrj.application.live-resize" value="true"/>
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<property name="com.apple.macos.smallTabs" value="true"/>
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</resources>
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<resources os="Mac" arch="i386">
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<property name="apple.awt.graphics.UseQuartz" value="false"/>
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<nativelib href="hdfnative-macintel.jar"/>
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</resources>
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<resources os="Mac" arch="ppc">
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<property name="apple.awt.graphics.UseQuartz" value="false"/>
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<nativelib href="hdfnative-macppc.jar"/>
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</resources>
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<resources os="Mac" arch="PowerPC">
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<property name="apple.awt.graphics.UseQuartz" value="false"/>
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<nativelib href="hdfnative-macppc.jar"/>
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</resources>
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<resources os="Windows">
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<property name="sun.java2d.noddraw" value="true"/>
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<nativelib href="hdfnative-win.jar"/>
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</resources>
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<resources os="Linux">
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<nativelib href="hdfnative-linux64.jar"/>
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</resources>
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<application-desc main-class="org.broad.igv.ui.IGVMainFrame">
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<argument>-g</argument>
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<argument>${fasta_file.url}</argument>
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</application-desc>
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</jnlp>
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]]>
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</param>
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<param type="data" name="fai_file" dataset="fasta_file" url="galaxy_${DATASET_HASH}.fasta.fai" format="fai" />
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<param type="template" name="redirect_url" strip="True" >
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#if $site_id.startswith( 'local_' )
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${site_link}?genome=${fasta_file.qp}&merge=true&name=name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
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#elif $site_id.startswith( 'web_link_' ):
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${site_link}?sessionURL=${fasta_file.qp}&genome=${fasta_file.qp}&merge=true&name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
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#else:
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${jnlp.url}
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#end if
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</param>
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</dynamic_links>
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<dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
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<!-- Our input data table is one line per dbkey -->
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<filter>${ $dataset.dbkey == $value }</filter>
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<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
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<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${fasta_file.qp}&genome=${fasta_file.dbkey}&merge=true&name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
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<param type="data" name="fasta_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
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</dynamic_links>
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</display>
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<!-- Dan Blankenberg -->
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@@ -0,0 +1,15 @@
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<tool id="CONVERTER_fasta_to_fai" name="Convert FASTA to fai file" version="1.0.0">
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<requirements>
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<requirement type="package" version="0.1.19">samtools</requirement>
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</requirements>
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<!--<command>samtools faidx '$input' && mv '${input}.fai' '$output' </command> -->
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<command><![CDATA[ln -s '$input' temp.fasta && samtools faidx temp.fasta && mv temp.fasta.fai '$output' && rm temp.fasta ]]></command>
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<inputs>
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<param name="input" type="data" format="fasta" label="Fasta file"/>
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</inputs>
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<outputs>
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<data name="output" format="fai"/>
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</outputs>
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<help>
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</help>
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</tool>
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