details: http://www.bx.psu.edu/hg/galaxy/rev/67dce52402fd changeset: 2942:67dce52402fd user: Nate Coraor <nate@bx.psu.edu> date: Mon Nov 02 16:21:28 2009 -0500 description: Remove old encode import tools diffstat: tools/data_source/encode_import.py | 82 ---------- tools/data_source/encode_import_all_latest_datasets.xml | 65 -------- tools/data_source/encode_import_chromatin_and_chromosomes.xml | 64 -------- tools/data_source/encode_import_code.py | 54 ------ tools/data_source/encode_import_gencode.xml | 67 -------- tools/data_source/encode_import_genes_and_transcripts.xml | 64 -------- tools/data_source/encode_import_multi-species_sequence_analysis.xml | 66 -------- tools/data_source/encode_import_transcription_regulation.xml | 65 -------- 8 files changed, 0 insertions(+), 527 deletions(-) diffs (565 lines): diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import.py --- a/tools/data_source/encode_import.py Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -#!/usr/bin/env python - -""" -Script that imports locally stored data as a new dataset for the user -Usage: import id outputfile -""" -import sys, os -from shutil import copyfile - -assert sys.version_info[:2] >= ( 2, 4 ) - -BUFFER = 1048576 - -def stop_err( msg ): - sys.stderr.write( msg ) - sys.exit() - -def main(): - uids = sys.argv[1].split(",") - out_file1 = sys.argv[2] - file_name = "%s/encode_datasets.loc" % sys.argv[3] - - #remove NONE from uids - have_none = True - while have_none: - try: - uids.remove('None') - except: - have_none = False - - #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files - available_files = {} - try: - for i, line in enumerate( file ( file_name ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( '\t' ) - try: - encode_group = fields[0].strip() - build = fields[1].strip() - description = fields[2].strip() - uid = fields[3].strip() - path = fields[4].strip() - try: - file_type = fields[5].strip() - except: - file_type = "bed" - except: - continue - available_files[uid] = ( description, path, build, file_type ) - except: - stop_err( "It appears that the configuration file for this tool is missing." ) - - #create list of tuples of ( displayName, FileName, build ) for desired files - desired_files = [] - for uid in uids: - try: - desired_files.append( available_files[uid] ) - except: - continue - - #copy first file to contents of given output file - file1_copied = False - while not file1_copied: - try: - first_file = desired_files.pop(0) - except: - stop_err( "There were no valid files requested." ) - file1_desc, file1_path, file1_build, file1_type = first_file - try: - copyfile( file1_path, out_file1 ) - print "#File1\t" + file1_desc + "\t" + file1_build + "\t" + file1_type - file1_copied = True - except: - stop_err( "The file '%s' is missing." %str( file1_path ) ) - - #Tell post-process filter where remaining files reside - for extra_output in desired_files: - file_desc, file_path, file_build, file_type = extra_output - print "#NewFile\t" + file_desc + "\t" + file_build + "\t" + file_path + "\t" + file_type - -if __name__ == "__main__": main() diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_all_latest_datasets.xml --- a/tools/data_source/encode_import_all_latest_datasets.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<tool id="encode_import_all_latest_datasets1" name="Combined Datasets"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="ALD" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="ALD" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_Al... - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_chromatin_and_chromosomes.xml --- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<tool id="encode_import_chromatin_and_chromosomes1" name="Chromatin and Chromosomes"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="CC" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="CC" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_Al... - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_code.py --- a/tools/data_source/encode_import_code.py Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -import os, sys - -from galaxy import datatypes, config, jobs -from shutil import copyfile - -#post processing, set build for data and add additional data to history -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - base_dataset = out_data.items()[0][1] - history = base_dataset.history - if history == None: - print "unknown history!" - return - new_stdout = "" - split_stdout = stdout.split("\n") - basic_name = "" - for line in split_stdout: - fields = line.split("\t") - if fields[0] == "#File1": - description = fields[1] - dbkey = fields[2] - file_type = fields[3] - name, data = out_data.items()[0] - data.set_size() - basic_name = data.name - data.name = data.name + " (" + description + ")" - data.dbkey = dbkey - data.info = data.name - data = app.datatypes_registry.change_datatype( data, file_type ) - data.init_meta() - data.set_peek() - app.model.flush() - elif fields[0] == "#NewFile": - description = fields[1] - dbkey = fields[2] - filepath = fields[3] - file_type = fields[4] - newdata = app.model.HistoryDatasetAssociation( create_dataset = True ) #This import should become a library - newdata.set_size() - newdata.extension = file_type - newdata.name = basic_name + " (" + description + ")" - history.add_dataset( newdata ) - app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) - app.model.flush() - try: - copyfile(filepath,newdata.file_name) - newdata.info = newdata.name - newdata.state = jobs.JOB_OK - except: - newdata.info = "The requested file is missing from the system." - newdata.state = jobs.JOB_ERROR - newdata.dbkey = dbkey - newdata.set_meta() - newdata.set_peek() - app.model.flush() diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_gencode.xml --- a/tools/data_source/encode_import_gencode.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -<tool id="encode_import_gencode1" name="Gencode Datasets"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GENCODE" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GENCODE" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -These are the datasets used for partitioning files. - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_Al... - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> - -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_genes_and_transcripts.xml --- a/tools/data_source/encode_import_genes_and_transcripts.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<tool id="encode_import_genes_and_transcripts1" name="Genes and Transcripts"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GT" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GT" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_Al... - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_multi-species_sequence_analysis.xml --- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -<tool id="encode_import_multi-species_sequence_analysis1" name="Multi-species Sequence Analysis"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="MSA" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="MSA" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_Al... - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_transcription_regulation.xml --- a/tools/data_source/encode_import_transcription_regulation.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<tool id="encode_import_transcription_regulation1" name="Transcription Regulation"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="TR" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="TR" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_Al... - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> - -</tool>