Mercurial > repos > devteam > picard
view picard_ReorderSam.xml @ 12:a459ead5ab75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
author | iuc |
---|---|
date | Thu, 13 Apr 2017 19:09:04 -0400 |
parents | 41b8d087a2d2 |
children | 486d7500da69 |
line wrap: on
line source
<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.0"> <description>reorder reads to match ordering in reference sequences</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( $reference_source.ref_file.fields.path ) #end if picard ReorderSam INPUT='$escaped_element_identifier' OUTPUT="${outFile}" REFERENCE="${ref_fasta}" ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR ]]></command> <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Load reference genome from"> <option value="cached">Local cache</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> <options from_data_table="picard_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> </when> </conditional> <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/> <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/> <expand macro="VS" /> </inputs> <outputs> <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> </outputs> <tests> <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> <param name="allow_incomplete_dict_concordance" value="false"/> <param name="allow_contig_length_discordance" value="false"/> <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help> .. class:: infomark **Purpose** ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. @dataset_collections@ ---- .. class:: warningmark Not to be confused with **SortSam**. @description@ ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs. By default, this tool requires a corresponding contig in the new reference for each read contig Default value: false. Possible values: {true, false} ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing. Default value: false. Possible values: {true, false} @more_info@ </help> </tool>