Mercurial > repos > fubar > rgrnastar_203e
changeset 4:94e775b41041 draft
fixed
| author | fubar |
|---|---|
| date | Fri, 09 Aug 2013 21:34:46 -0400 |
| parents | 00ab5d9c061f |
| children | fc3b5f4ff4c4 |
| files | prepStar.sh rg_rnaStar.xml rgrnastar/prepStar.sh rgrnastar/rg_rnaStar.xml rgrnastar/tool-data/rnastar_indices.loc.sample rgrnastar/tool_data_table_conf.xml.sample rgrnastar/tool_dependencies.xml tool-data/rnastar_indices.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 10 files changed, 280 insertions(+), 278 deletions(-) [+] |
line wrap: on
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--- a/prepStar.sh Fri Aug 09 05:13:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -# automate their generation f -# from existing fasta genomes -INDEXROOT=/data/ucsc -# fix that -for genome in hg19 hg18 mm9 mm10 rn4 rn5 -do - TARGET=${INDEXROOT}/${genome}/rnastar - mkdir -p $TARGET - cd $TARGET - STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${TARGET}/$genome.fa --runThreadN 4 -done -
--- a/rg_rnaStar.xml Fri Aug 09 05:13:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,219 +0,0 @@ -<tool id="rna_star" name="RNA-STAR" version="0.2"> - <description>Gapped-read mapper for RNA-seq data</description> - <requirements> - <requirement type="package" version="2.3.0e">rnastar</requirement> - <requirement type="package">samtools</requirement> - </requirements> - <command> - ## - ## Run STAR. - ## - - STAR - ## Can adjust this as appropriate for the system. - --genomeLoad NoSharedMemory - - --genomeDir ${refGenomeSource.index.fields.path} - --readFilesIn $input1 - #if $singlePaired.sPaired == "paired" - $singlePaired.input2 - #end if - - --runThreadN 4 - - ## Parameters. - #if $params.settingsType == "full": - --chimSegmentMin $params.chim_segment_min - --chimScoreMin $params.chim_score_min - #end if - - ## Needed to generate SAM tags for Cufflinks tools. - --outSAMstrandField intronMotif - - ; - - ## - ## BAM conversion. - ## - - ## Convert aligned reads. - samtools view -Shb Aligned.out.sam | samtools sort - Aligned.out - - ## Convert chimeric reads. - #if $params.settingsType == "full" and $params.chim_segment_min > 0: - ; samtools view -Shb Chimeric.out.sam | samtools sort - Chimeric.out - #end if - </command> - - <stdio> - <regex match=".*" source="both" level="warning" description="generic stdout/err chatter"/> - </stdio> - - <inputs> - <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)" - help="Only letters, numbers and underscores (_) will be retained in this field"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value="_" /> </valid> - </sanitizer> - </param> - <!-- FASTQ input(s) and options specifically for paired-end data. --> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Single ended or mate-pair ended reads in this library?"> - <option value="single" selected="true">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/> - </when> - <when value="paired"> - <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> - <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> - </when> - </conditional> - - <!-- Genome source. --> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome"> - <options from_data_table="rnastar_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> - </when> - </conditional> - - <!-- Parameter settings. --> - <conditional name="params"> - <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR parameter."> - <option value="preSet" selected="true">Use Defaults</option> - <option value="full">Full parameter list</option> - </param> - <when value="preSet" /> - <!-- Full/advanced params. --> - <when value="full"> - <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" /> - <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" /> - </when> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="output_log" label="${on_string}_{jobName}.log" from_work_dir="Log.final.out"/> - <data format="interval" name="chimeric_junctions" label="${on_string}_{jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction"> - <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="star_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="bam" name="chimeric_reads" label="${on_string}_{jobName}_starmappedchim.bam" - from_work_dir="Chimeric.out.bam"> - <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="star_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="interval" name="splice_junctions" label="${on_string}_{jobName}_starsplicejunct.bed" - from_work_dir="SJ.out.tab"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="star_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="bam" name="mapped_reads" label="${on_string}_{jobName}_starmapped.bam" - from_work_dir="Aligned.out.bam"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="star_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - </outputs> -<help> - -**Attributions** - -Note that each component has its own license. Good luck with figuring out your obligations. - -rna_star - see the web site at rna_star_ - -For details, please see the rna_starMS_ -"STAR: ultrafast universal RNA-seq aligner" -A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 - -Galaxy_ (that's what you are using right now!) for gluing everything together - -Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper - -Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies -and odds and ends of other code and documentation comprising this tool was -written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts - -.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml -.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/ -.. _rna_star: http://code.google.com/p/rna-star/ -.. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full -.. _Galaxy: http://getgalaxy.org - -</help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgrnastar/prepStar.sh Fri Aug 09 21:34:46 2013 -0400 @@ -0,0 +1,12 @@ +# automate their generation f +# from existing fasta genomes +INDEXROOT=/data/ucsc +# fix that +for genome in hg19 hg18 mm9 mm10 rn4 rn5 +do + TARGET=${INDEXROOT}/${genome}/rnastar + mkdir -p $TARGET + cd $TARGET + STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${TARGET}/$genome.fa --runThreadN 4 +done +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgrnastar/rg_rnaStar.xml Fri Aug 09 21:34:46 2013 -0400 @@ -0,0 +1,219 @@ +<tool id="rna_star" name="RNA-STAR" version="0.2"> + <description>Gapped-read mapper for RNA-seq data</description> + <requirements> + <requirement type="package" version="2.3.0e">rnastar</requirement> + <requirement type="package">samtools</requirement> + </requirements> + <command> + ## + ## Run STAR. + ## + + STAR + ## Can adjust this as appropriate for the system. + --genomeLoad NoSharedMemory + + --genomeDir ${refGenomeSource.index.fields.path} + --readFilesIn $input1 + #if $singlePaired.sPaired == "paired" + $singlePaired.input2 + #end if + + --runThreadN 4 + + ## Parameters. + #if $params.settingsType == "full": + --chimSegmentMin $params.chim_segment_min + --chimScoreMin $params.chim_score_min + #end if + + ## Needed to generate SAM tags for Cufflinks tools. + --outSAMstrandField intronMotif + + ; + + ## + ## BAM conversion. + ## + + ## Convert aligned reads. + samtools view -Shb Aligned.out.sam | samtools sort - Aligned.out + + ## Convert chimeric reads. + #if $params.settingsType == "full" and $params.chim_segment_min > 0: + ; samtools view -Shb Chimeric.out.sam | samtools sort - Chimeric.out + #end if + </command> + + <stdio> + <regex match=".*" source="both" level="warning" description="generic stdout/err chatter"/> + </stdio> + + <inputs> + <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)" + help="Only letters, numbers and underscores (_) will be retained in this field"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="_" /> </valid> + </sanitizer> + </param> + <!-- FASTQ input(s) and options specifically for paired-end data. --> + <conditional name="singlePaired"> + <param name="sPaired" type="select" label="Single ended or mate-pair ended reads in this library?"> + <option value="single" selected="true">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/> + </when> + <when value="paired"> + <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> + <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> + </when> + </conditional> + + <!-- Genome source. --> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome"> + <options from_data_table="rnastar_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> + </when> + </conditional> + + <!-- Parameter settings. --> + <conditional name="params"> + <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR parameter."> + <option value="preSet" selected="true">Use Defaults</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> + <!-- Full/advanced params. --> + <when value="full"> + <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" /> + <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" /> + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="output_log" label="${on_string}_{jobName}.log" from_work_dir="Log.final.out"/> + <data format="interval" name="chimeric_junctions" label="${on_string}_{jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction"> + <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="star_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="bam" name="chimeric_reads" label="${on_string}_{jobName}_starmappedchim.bam" + from_work_dir="Chimeric.out.bam"> + <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="star_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="interval" name="splice_junctions" label="${on_string}_{jobName}_starsplicejunct.bed" + from_work_dir="SJ.out.tab"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="star_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="bam" name="mapped_reads" label="${on_string}_{jobName}_starmapped.bam" + from_work_dir="Aligned.out.bam"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="star_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data> + </outputs> +<help> + +**Attributions** + +Note that each component has its own license. Good luck with figuring out your obligations. + +rna_star - see the web site at rna_star_ + +For details, please see the rna_starMS_ +"STAR: ultrafast universal RNA-seq aligner" +A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 + +Galaxy_ (that's what you are using right now!) for gluing everything together + +Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper + +Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies +and odds and ends of other code and documentation comprising this tool was +written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts + +.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml +.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/ +.. _rna_star: http://code.google.com/p/rna-star/ +.. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full +.. _Galaxy: http://getgalaxy.org + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgrnastar/tool-data/rnastar_indices.loc.sample Fri Aug 09 21:34:46 2013 -0400 @@ -0,0 +1,16 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of rna-star indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie2_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +hg19 hg19 hg19 full /data/ucsc/hg19/rnastar +hg18 hg18 hg18 full /data/ucsc/hg18/rnastar +mm9 mm9 mm9 full /data/ucsc/mm9/rnastar +mm10 mm10 mm10 full /data/ucsc/mm10/rnastar +rn4 rn4 rn4 full /data/ucsc/rn4/rnastar +rn5 rn5 rn5 full /data/ucsc/rn5/rnastar +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgrnastar/tool_data_table_conf.xml.sample Fri Aug 09 21:34:46 2013 -0400 @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="rnastar_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/rnastar_indices.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgrnastar/tool_dependencies.xml Fri Aug 09 21:34:46 2013 -0400 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="rnastar" version="2.3.0e"> + <install version="1.0"> + <actions> + <action type="make_directory">$INSTALL_DIR</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="download_by_url" target_filename="STAR_2.3.0e.tar.gz">http://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action> + <action type="shell_command">cp -r ./* /tmp/test</action> + <action type="shell_command">echo `ls -lt` > /tmp/lslt</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>STAR</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +Installs the STAR binary for rnastar - see https://code.google.com/p/rna-star/ + </readme> + </package> +</tool_dependency> +
--- a/tool-data/rnastar_indices.loc.sample Fri Aug 09 05:13:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of rna-star indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie2_indices.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> -# -hg19 hg19 hg19 full /data/ucsc/hg19/rnastar -hg18 hg18 hg18 full /data/ucsc/hg18/rnastar -mm9 mm9 mm9 full /data/ucsc/mm9/rnastar -mm10 mm10 mm10 full /data/ucsc/mm10/rnastar -rn4 rn4 rn4 full /data/ucsc/rn4/rnastar -rn5 rn5 rn5 full /data/ucsc/rn5/rnastar -
--- a/tool_data_table_conf.xml.sample Fri Aug 09 05:13:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <table name="rnastar_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/rnastar_indices.loc" /> - </table> -</tables>
--- a/tool_dependencies.xml Fri Aug 09 05:13:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="rnastar" version="2.3.0e"> - <install version="1.0"> - <actions> - <action type="make_directory">$INSTALL_DIR</action> - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="download_by_url">https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>STAR</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Installs the STAR binary for rnastar - see https://code.google.com/p/rna-star/ - </readme> - </package> -</tool_dependency> -