Mercurial > repos > devteam > picard
diff picard_ReorderSam.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_ReorderSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_ReorderSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,26 +1,28 @@ -<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> +<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> <description>reorder reads to match ordering in reference sequences</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">0</token> </macros> <xrefs> <xref type="bio.tools">picard_reordersam</xref> </xrefs> - <expand macro="requirements" /> + <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}" "${ref_fasta}" && + ln -sf '${reference_source.ref_file}' '${ref_fasta}' && #if str( $reference_source.reference_source_selector ) == "history": - picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" - QUIET=true - VERBOSITY=ERROR + picard CreateSequenceDictionary + --REFERENCE '${ref_fasta}' + --OUTPUT '${picard_dict}' + --QUIET true + --VERBOSITY ERROR && @@ -32,61 +34,55 @@ picard ReorderSam - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" - REFERENCE="${ref_fasta}" - ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" - ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --SEQUENCE_DICTIONARY '${ref_fasta}' + --ALLOW_INCOMPLETE_DICT_CONCORDANCE '${allow_incomplete_dict_concordance}' + --ALLOW_CONTIG_LENGTH_DISCORDANCE '${allow_contig_length_discordance}' - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR + --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> + <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,bam,sam" label="Use the following dataset to create dictionary" help="You can upload sequences to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/> + </when> + </conditional> + <param name="inputFile" type="data" format="sam,bam" 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 @@ -116,5 +112,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>