<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.1"> <description>converts SAM format to BAM format</description> <requirements> <requirement type="package">samtools</requirement> </requirements> <command interpreter="python"> sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} #if $source.index_source == "history": --ref_file=$source.ref_file #else --ref_file="None" #end if --output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR} </command> <inputs> <conditional name="source"> <param name="index_source" type="select" label="Choose the source for the reference list"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="input1" type="data" format="sam" label="SAM File to Convert"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build.