Mercurial > repos > iuc > data_manager_star_index_builder
diff data_manager/rna_star_index_builder.xml @ 6:64deddb6a8ec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author | iuc |
---|---|
date | Thu, 28 Nov 2019 15:48:56 -0500 |
parents | f5eb9afa8f8a |
children | 6c6c6df09e64 |
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--- a/data_manager/rna_star_index_builder.xml Thu Aug 15 11:30:16 2019 -0400 +++ b/data_manager/rna_star_index_builder.xml Thu Nov 28 15:48:56 2019 -0500 @@ -1,11 +1,13 @@ -<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="2.7.1a" profile="17.01"> +<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="@IDX_VERSION@+galaxy2" profile="19.05"> <description>builder</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="3.7">python</requirement> + </expand> <command><![CDATA[ if [ -z "\$GALAXY_MEMORY_MB" ] ; then @@ -14,17 +16,16 @@ GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ; fi ; -#import json, os -#set params = json.loads(open(str($out_file)).read()) -#set target_directory = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') -#set subdir = os.path.basename(target_directory) +#import os +#set $target_directory = str($out_file.extra_files_path) +#set $subdir = os.path.basename($target_directory) -mkdir -p '${target_directory}/${subdir}' && +mkdir '${target_directory}' && STAR --runMode genomeGenerate --genomeFastaFiles '${all_fasta_source.fields.path}' ---genomeDir '${target_directory}/${subdir}' +--genomeDir '${target_directory}' --limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES} #if $GTFconditional.GTFselect == "withGTF": --sjdbGTFfile '${GTFconditional.sjdbGTFfile}' @@ -100,25 +101,26 @@ <data name="out_file" format="data_manager_json"/> </outputs> - <!-- not available in planemo at the moment of writing <tests> <test> - <param name="all_fasta_source" value="phiX.fa"/> + <param name="all_fasta_source" value="phiX174"/> <param name="sequence_name" value="phiX"/> <param name="sequence_id" value="minimal-settings"/> <param name="modelformat" value="None"/> - <output name="out_file" file="test_star_01.data_manager_json"/> + <output name="out_file" file="test_star_01.data_manager_json" compare="re_match"/> </test> </tests> - --> <help><![CDATA[ .. class:: infomark *What it does* -This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner. +This is a Galaxy data manager tool for the gap-aware RNA aligner STAR. + +This version of the tool builds STAR indices of the format first introduced +with STAR version @IDX_VERSION@. Please read the fine manual - that and the google group are the places to learn about the options above.