Mercurial > repos > iuc > data_manager_star_index_builder
changeset 7:6c6c6df09e64 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
| author | iuc |
|---|---|
| date | Wed, 05 Aug 2020 09:38:12 -0400 |
| parents | 64deddb6a8ec |
| children | d3879aceba04 |
| files | data_manager/macros.xml data_manager/rna_star_index_builder.xml data_manager_conf.xml test-data/test_star_01.data_manager_json tool-data/rnastar_index2_versioned.loc.sample tool-data/rnastar_index2x_versioned.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 7 files changed, 61 insertions(+), 85 deletions(-) [+] |
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--- a/data_manager/macros.xml Thu Nov 28 15:48:56 2019 -0500 +++ b/data_manager/macros.xml Wed Aug 05 09:38:12 2020 -0400 @@ -5,7 +5,7 @@ the index versions in sync, but you should manually adjust the +galaxy version number. --> <!-- STAR version to be used --> - <token name="@VERSION@">2.7.2b</token> + <token name="@VERSION@">2.7.5b</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected by the current version. @@ -13,7 +13,8 @@ STAR -h | grep versionGenome or by looking for the versionGenome parameter in source/parametersDefault of STAR's source code --> - <token name="@IDX_VERSION@">2.7.1a</token> + <token name="@IDX_VERSION@">2.7.4a</token> + <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token> <xml name="requirements"> <requirements> @@ -27,7 +28,7 @@ <param argument="--genomeDir" name="genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="rnastar_index2_versioned"> + <options from_data_table="@IDX_DATA_TABLE@"> <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> <filter type="static_value" column="5" value="@IDX_VERSION@" /> <filter type="sort_by" column="2" /> @@ -53,7 +54,7 @@ <conditional name="refGenomeSource.geneSource"> <when value="indexed"> <action type="metadata" name="dbkey"> - <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0"> + <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> </option> @@ -76,10 +77,21 @@ --genomeDir 'tempstargenomedir' --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}' ## Handle difference between indices with/without annotations - #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': - --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' - --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' - #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': + #if 'GTFconditional' in $refGenomeSource: + ## GTFconditional exists only in STAR, but not STARsolo + #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': + --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' + --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' + #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': + --sjdbGTFtagExonParentTranscript Parent + #end if + #end if + #else: + ## ref genome selection is less complex for STARsolo cause + ## with-gtf is mandatory there + --sjdbOverhang '${refGenomeSource.sjdbOverhang}' + --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}' + #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3': --sjdbGTFtagExonParentTranscript Parent #end if #end if @@ -110,6 +122,13 @@ #end if #end if ]]></token> + <xml name="ref_selection"> + <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> + <!-- Currently, this parameter is not exposed in the wrapper, + but used only in the tests to avoid excessive index sizes for + the tiny test genomes. --> + <param name="genomeSAindexNbases" type="hidden" value="" /> + </xml> <xml name="stdio" > <stdio> <regex match="FATAL error" source="both" level="fatal"/> @@ -119,48 +138,4 @@ <yield /> </stdio> </xml> - <xml name="refgenomehandling" > - <conditional name="refGenomeSource"> - <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options"> - <option value="indexed" selected="true">Use a built-in index</option> - <option value="history">Use reference genome from history and create temporary index</option> - </param> - <when value="indexed"> - <conditional name="GTFconditional"> - <param name="GTFselect" type="select" - label="Reference genome with or without an annotation" - help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions."> - <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> - <option value="with-gtf">use genome reference with builtin gene-model</option> - </param> - <when value="with-gtf"> - <expand macro="index_selection" with_gene_model="1" /> - </when> - <when value="without-gtf"> - <expand macro="index_selection" with_gene_model="0" /> - <expand macro="@SJDBOPTIONS@" /> - </when> - </conditional> - </when> - <when value="history"> - <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> - <!-- Currently, this parameter is not exposed in the wrapper, - but used only in the tests to avoid excessive index sizes for - the tiny test genomes. --> - <param name="genomeSAindexNbases" type="hidden" value="" /> - <conditional name="GTFconditional"> - <param name="GTFselect" type="select" - label="Build index with our without known splice junctions annotation" - help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome."> - <option value="without-gtf">build index without gene-model</option> - <option value="with-gtf">build index with gene-model</option> - </param> - <when value="with-gtf"> - <expand macro="@SJDBOPTIONS@" optional="false"/> - </when> - <when value="without-gtf" /> - </conditional> - </when> - </conditional> - </xml> </macros>
--- a/data_manager/rna_star_index_builder.xml Thu Nov 28 15:48:56 2019 -0500 +++ b/data_manager/rna_star_index_builder.xml Wed Aug 05 09:38:12 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="@IDX_VERSION@+galaxy2" profile="19.05"> +<tool id="rna_star_index_builder_data_manager" name="rnastar index versioned" tool_type="manage_data" version="@IDX_VERSION@" profile="19.05"> <description>builder</description> <macros> @@ -51,7 +51,7 @@ #if str($GTFconditional.GTFselect) == "withGTF": --with-gene-model #end if ---data-table rnastar_index2_versioned +--data-table @IDX_DATA_TABLE@ --subdir '${subdir}' ]]></command> <inputs>
--- a/data_manager_conf.xml Thu Nov 28 15:48:56 2019 -0500 +++ b/data_manager_conf.xml Wed Aug 05 09:38:12 2020 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder" version="0.0.6"> - <data_table name="rnastar_index2_versioned"> + <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder" version="0.0.7"> + <data_table name="rnastar_index2x_versioned"> <output> <column name="value" /> <column name="dbkey" />
--- a/test-data/test_star_01.data_manager_json Thu Nov 28 15:48:56 2019 -0500 +++ b/test-data/test_star_01.data_manager_json Wed Aug 05 09:38:12 2020 -0400 @@ -1,1 +1,1 @@ -{"data_tables": {"rnastar_index2_versioned": \[{"dbkey": "phiX174", "name": "phiX174", "path": ".*", "value": "phiX174", "version": "2.7.1a", "with_gene_model": "0"}\]}} \ No newline at end of file +{"data_tables": {"rnastar_index2x_versioned": \[{"dbkey": "phiX174", "name": "phiX174", "path": ".*", "value": "phiX174", "version": "2.7.4a", "with_gene_model": "0"}\]}}
--- a/tool-data/rnastar_index2_versioned.loc.sample Thu Nov 28 15:48:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +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 rnastar_index2.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The rnastar_index2.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> -# -#The <with_gene_model> column should be 1 or 0, indicating whether the index -#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) -#or not. -# -#The <version> column indicates the STAR version that introduced the format of -#the index, i.e., the oldest STAR version that could make use of the index. -# -#Note that STAR indices can become quite large. Consequently, it is only -#advisable to create indices with annotations if it's known ahead of time that -#(A) the annotations won't be frequently updated and (B) the read lengths used -#will also rarely vary. If either of these is not the case, it's advisable to -#create indices without annotations and then specify an annotation file and -#maximum read length (minus 1) when running STAR. -# -#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a -#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnastar_index2x_versioned.loc.sample Wed Aug 05 09:38:12 2020 -0400 @@ -0,0 +1,27 @@ +#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 +#rnastar_index2x_versioned.loc file similar to this one (store it in this +directory) that points to the directories in which those files are stored. +#The rnastar_index2x_versioned.loc file has this format (longer white space +#characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> +# +#The <with_gene_model> column should be 1 or 0, indicating whether the index +#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) +#or not. +# +#The <version> column indicates the STAR version that introduced the format of +#the index, i.e., the oldest STAR version that could make use of the index. +# +#Note that STAR indices can become quite large. Consequently, it is only +#advisable to create indices with annotations if it's known ahead of time that +#(A) the annotations won't be frequently updated and (B) the read lengths used +#will also rarely vary. If either of these is not the case, it's advisable to +#create indices without annotations and then specify an annotation file and +#maximum read length (minus 1) when running STAR. +# +#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a +#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a +
--- a/tool_data_table_conf.xml.sample Thu Nov 28 15:48:56 2019 -0500 +++ b/tool_data_table_conf.xml.sample Wed Aug 05 09:38:12 2020 -0400 @@ -5,8 +5,8 @@ <file path="tool-data/all_fasta.loc" /> </table> <!-- Locations of STAR indexes --> - <table name="rnastar_index2_versioned" comment_char="#" allow_duplicate_entries="False"> + <table name="rnastar_index2x_versioned" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path, with_gene_model, version</columns> - <file path="tool-data/rnastar_index2_versioned.loc" /> + <file path="tool-data/rnastar_index2x_versioned.loc" /> </table> </tables>