Mercurial > repos > devteam > picard
view picard_BedToIntervalList.xml @ 13:c7dd8d7946b8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
author | iuc |
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date | Sat, 20 Jan 2018 08:28:02 -0500 |
parents | 41b8d087a2d2 |
children | 486d7500da69 |
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<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.0"> <description>convert coordinate data into picard interval list format</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ #set $picard_dict = "localref.dict" #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension ln -s "${reference_source.ref_file}" "${ref_fasta}" && #if str( $reference_source.reference_source_selector ) == "history": picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR && #else: #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa) #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict #end if picard BedToIntervalList INPUT='$escaped_element_identifier' OUTPUT="${outFile}" SEQUENCE_DICTIONARY="${picard_dict}" QUIET=true VERBOSITY=ERROR ]]></command> <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Load picard dictionary file from"> <option value="cached">Local cache</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> <options from_data_table="picard_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> </when> </conditional> <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" /> </inputs> <outputs> <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list"> </data> </outputs> <tests> <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" /> <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/> <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" /> </test> </tests> <help> .. class:: infomark **Purpose** Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format. @dataset_collections@ @description@ SEQUENCE_DICTIONARY=File SD=File The sequence dictionary. You can either use dictionary pre-cached on this instance of Galaxy, or create one on teh fly from a FASTA file uploaded to history (right pane of the interface). @more_info@ </help> </tool>