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comparison macros.xml @ 8:55e8a08e39e1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
author iuc
date Tue, 03 Feb 2026 18:50:29 +0000
parents 04253ade1697
children
comparison
equal deleted inserted replaced
7:91d37702c47b 8:55e8a08e39e1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">4.1.7.0</token> 3 <token name="@TOOL_VERSION@">4.6.2.0</token>
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">24.1</token>
5 6
6 <xml name="requirements"> 7 <xml name="requirements">
7 <requirements> 8 <requirements>
8 <requirement type="package" version="@VERSION@">gatk4</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">gatk4</requirement>
9 <requirement type="package" version="0.2.5">tabix</requirement> 10 <requirement type="package" version="1.11">tabix</requirement>
10 <requirement type="package" version="1.9">samtools</requirement> 11 <requirement type="package" version="1.23">samtools</requirement>
11 <yield /> 12 <yield />
12 </requirements> 13 </requirements>
13 </xml> 14 </xml>
14 15
15 <!--Hacky way to determine GATK version, for display in tool info--> 16 <!--Hacky way to determine GATK version, for display in tool info-->
652 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}--> 653 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}-->
653 <!--#end if--> 654 <!--#end if-->
654 <!--#end if--> 655 <!--#end if-->
655 <!--</template>--> 656 <!--</template>-->
656 657
658 <token name="@GATK_LINK_REF@"><![CDATA[
659 ## 1. Link Reference Genome
660 #if $reference_source.reference_source_selector == "history":
661 ln -s '$reference_source.reference_sequence' reference.fa &&
662 samtools faidx reference.fa &&
663 #else:
664 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
665 ln -s '${reference_source.reference_sequence.fields.path}.fai' reference.fa.fai &&
666 #end if
667
668 ## Ensure dictionary exists
669 gatk CreateSequenceDictionary -R reference.fa &&
670 ]]></token>
671
672 <xml name="gatk_ref_source">
673 <conditional name="reference_source">
674 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
675 <option value="cached">Locally cached</option>
676 <option value="history" selected="true">History</option>
677 </param>
678 <when value="cached">
679 <param name="reference_sequence" type="select" label="Reference" help="Select reference genome">
680 <options from_data_table="all_fasta" />
681 </param>
682 </when>
683 <when value="history">
684 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Select reference genome from history" />
685 </when>
686 </conditional>
687 </xml>
688
689 <xml name="gatk_param_intervals">
690 <param name="intervals" argument="-L" type="data" format="picard_interval_list" optional="true" label="Interval List" help="One or more genomic intervals over which to operate." />
691 </xml>
692
693 <xml name="gatk_param_known_sites">
694 <param argument="--known-sites" type="data" format="vcf_bgzip" multiple="true" label="Known Sites" help="VCF file(s) (e.g., dbSNP, Mills) masking known sites." />
695 </xml>
696
697 <xml name="gatk_param_use_original_qualities">
698 <param argument="--use-original-qualities" type="boolean" truevalue="--use-original-qualities" falsevalue="" checked="true" label="Use Original Qualities" help="Use the OQ tag if present." />
699 </xml>
700
701 <xml name="gatk_param_add_output_sam_program_record">
702 <param argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" checked="true" label="Add Output SAM Program Record" help="Adds an extra PG tag to the header." />
703 </xml>
657 704
658 <!--Citations--> 705 <!--Citations-->
659 <xml name="citations"> 706 <xml name="citations">
660 <citation type="doi">10.1101/gr.107524.110</citation> 707 <citation type="doi">10.1101/gr.107524.110</citation>
661 <citation type="doi">10.1038/ng.806</citation> 708 <citation type="doi">10.1038/ng.806</citation>