Mercurial > repos > devteam > picard
diff picard_BedToIntervalList.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_BedToIntervalList.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_BedToIntervalList.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,23 +1,25 @@ -<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>convert coordinate data into picard interval list format</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ +<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>convert coordinate data into picard interval list format</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </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}" "${ref_fasta}" && + ln -sf '${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 '${picard_dict}' + -QUIET true + -VERBOSITY ERROR && @@ -30,54 +32,48 @@ picard BedToIntervalList - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' - SEQUENCE_DICTIONARY="${picard_dict}" - QUIET=true - VERBOSITY=ERROR + --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 ${on_string}: Picard interval list"> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load picard dictionary file from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> + <options from_data_table="picard_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available"/> + </options> + <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/> + </when> + </conditional> + <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset"/> + </inputs> + <outputs> + <data name="outFile" format="picard_interval_list" label="${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> + </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 @@ -97,5 +93,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>