1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/04e8ed0cd930/ changeset: 04e8ed0cd930 user: dan date: 2011-11-29 23:30:14 summary: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools. affected #: 13 files

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -2,7 +2,7 @@ <description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> megablast_wrapper.py - --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" + --db_build="${source_select.fields.path}" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -19,7 +19,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes_color' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if

## Are reads single-end or paired?

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -17,7 +17,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if

## Are reads single-end or paired?

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -4,7 +4,7 @@ <command interpreter="python"> ngs_simulation.py #if $in_type.input_type == "built-in" - --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }" + --input="${in_type.genome.fields.path}" --genome=$in_type.genome #else --input=$in_type.input1

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -6,7 +6,7 @@ #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${genomeSource.index.fields.path}" #end if </command><requirements><requirement type="package">picard</requirement></requirements>

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -11,9 +11,9 @@ $s.sourceOfRef.ref #else #if $s.space == "color" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path" #end if #end if #if $s.mate.singleOrPairs == "single":

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -58,7 +58,7 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single":

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -61,8 +61,7 @@ #end if #else ##use pre-built index - ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" - --ref="${ refGenomeSource.index.fields.path }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single":

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ b/tools/sr_mapping/bwa_color_wrapper.xml @@ -14,7 +14,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes_color' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -17,7 +17,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_paired_reads_wrapper.xml --- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" #end if --output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR}

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" --ref_sequences="None" #end if #if $params.source_select=="pre_set":

diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -13,7 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${genomeSource.indexReference.fields.path} #else: $genomeSource.historyReference #end if

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