Mercurial > repos > iuc > data_manager_hisat2_index_builder
diff data_manager/hisat2_index_builder.xml @ 8:e4f36467bb51 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd
| author | iuc |
|---|---|
| date | Sat, 16 Aug 2025 14:36:15 +0000 |
| parents | 8eac26f44d29 |
| children |
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--- a/data_manager/hisat2_index_builder.xml Sun Apr 16 08:30:13 2023 +0000 +++ b/data_manager/hisat2_index_builder.xml Sat Aug 16 14:36:15 2025 +0000 @@ -1,9 +1,15 @@ -<tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.1.0" profile="19.05"> +<tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>builder</description> + <macros> + <token name="@WRAPPER_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> <requirements> - <requirement type="package" version="2.1.0">hisat2</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">hisat2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + #set $value = $sequence_id or $all_fasta_source.fields.dbkey + #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: ln -s '${advanced.gtf_input}' gtf_file.gtf && hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt && @@ -17,30 +23,53 @@ hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted && #end if #end if - python '$__tool_directory__/hisat2_index_builder.py' --output '${out_file}' - --fasta_filename '${all_fasta_source.fields.path}' - --fasta_dbkey '${all_fasta_source.fields.dbkey}' - --fasta_description '${all_fasta_source.fields.name}' - --data_table_name hisat2_indexes - --indexer_options "-p \${GALAXY_SLOTS:-1} + + mkdir -p '${out_file.extra_files_path}' && + ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && + working="\$(pwd)" && + cd '${out_file.extra_files_path}' && + + hisat2-build -p "\${GALAXY_SLOTS:-1}" #if $advanced.adv_param_select == 'yes': --noauto #if $advanced.snps: - --snps "`pwd`/extracted.snp" - --haplotype "`pwd`/extracted.haplotype" + --snp "\${working}/extracted.snp" + --haplotype "\${working}/extracted.haplotype" #end if #if $advanced.gtf_input: - --ss "`pwd`/splice_sites.txt" - --exon "`pwd`/exon.txt" + --ss "\${working}/splice_sites.txt" + --exon "\${working}/exon.txt" #end if --bmax $advanced.bmax --bmaxdivn $advanced.bmaxdivn --dcv $advanced.dcv --offrate $advanced.offrate #end if - " + '${fasta_file_name}' '${value}' && + rm '${out_file.extra_files_path}/${fasta_file_name}' && + + cp '$dmjson' '$out_file' ]]> </command> + <configfiles> + <configfile name="dmjson"><![CDATA[#slurp +#set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] +#set $value = $sequence_id or $all_fasta_source.fields.dbkey +#set $name = $sequence_name or $all_fasta_source.fields.name +{ + "data_tables":{ + "hisat2_indexes":[ + { + "value": "${value}", + "dbkey": "${all_fasta_source.fields.dbkey}", + "name": "${name}", + "path": "${value}" + } + ] + } +} +]]></configfile> + </configfiles> <inputs> <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> <options from_data_table="all_fasta" /> @@ -69,7 +98,18 @@ <tests> <test> <param name="all_fasta_source" value="phiX174"/> - <output name="out_file" file="hisat2_data_manager.json"/> + <output name="out_file" file="hisat2_data_manager.1.json"/> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="sequence_name" value="Galeocerdo cuvier"/> + <param name="sequence_id" value="tigHai1"/> + <param name="advanced|adv_param_select" value="yes"/> + <param name="advanced|bmax" value="3"/> + <param name="advanced|bmaxdivn" value="3"/> + <param name="advanced|dcv" value="4"/> + <param name="advanced|offrate" value="5"/> + <output name="out_file" file="hisat2_data_manager.2.json"/> </test> </tests> <help>