Mercurial > repos > devteam > sam_pileup
diff sam_pileup.xml @ 1:e7d863c5c5d6
Update sam_pileup to use the fasta_indexes data table.
author | Dave Bouvier <dave@bx.psu.edu> |
---|---|
date | Wed, 11 Dec 2013 12:54:32 -0500 |
parents | 95612c159681 |
children | 3ff8935743a9 |
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--- a/sam_pileup.xml Mon Aug 26 14:21:12 2013 -0400 +++ b/sam_pileup.xml Wed Dec 11 12:54:32 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="sam_pileup" name="Generate pileup" version="1.1.1"> +<tool id="sam_pileup" name="Generate pileup" version="1.1.2"> <description>from BAM dataset</description> <requirements> <requirement type="package" version="0.1.16">samtools</requirement> @@ -11,7 +11,7 @@ #if $refOrHistory.reference == "history": --ownFile=$refOrHistory.ownFile #else: - --ownFile="None" + --index=${refOrHistory.index.fields.path} #end if --dbkey=${input1.metadata.dbkey} --indexDir=${GALAXY_DATA_INDEX_DIR} @@ -41,7 +41,14 @@ <when value="indexed"> <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> <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." line_startswith="index" /> + <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + + </param> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input1" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> </param> </when> <when value="history"> @@ -100,6 +107,7 @@ --> <param name="reference" value="indexed" /> <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> + <param name="index" value="chr_m" /> <param name="lastCol" value="no" /> <param name="indels" value="no" /> <param name="mapCap" value="60" />