Previous changeset 6:820754ab8901 (2015-10-20) Next changeset 8:583abf29fc8e (2017-05-09) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
modified:
samtools_mpileup.xml |
b |
diff -r 820754ab8901 -r bfc4517aa037 samtools_mpileup.xml --- a/samtools_mpileup.xml Tue Oct 20 16:24:54 2015 -0400 +++ b/samtools_mpileup.xml Wed Nov 11 12:53:32 2015 -0500 |
[ |
@@ -1,4 +1,4 @@ -<tool id="samtools_mpileup" name="MPileup" version="2.1"> +<tool id="samtools_mpileup" name="MPileup" version="2.1.1"> <description>call variants</description> <macros> <import>macros.xml</import> @@ -18,8 +18,8 @@ #else: -f "${reference_source.ref_file}" #end if - #for $i, $input_bam in enumerate( $reference_source.input_bams ): - "${input_bam.input_bam}" + #for $bam in $reference_source.input_bam: + "${bam}" #end for #if str( $advanced_options.advanced_options_selector ) == "advanced": #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter": @@ -50,14 +50,14 @@ #if str( $advanced_options.region_string ): -r "${advanced_options.region_string}" #end if - + #end if #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation': ## ${genotype_likelihood_computation_type.output_format} ${genotype_likelihood_computation_type.compressed} - + #if str( $genotype_likelihood_computation_type.output_tags ) != "None": --output-tags "${genotype_likelihood_computation_type.output_tags}" #end if @@ -77,8 +77,8 @@ #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling': -I #end if - - + + #else: ${genotype_likelihood_computation_type.base_position_on_reads} ${genotype_likelihood_computation_type.output_mapping_quality} @@ -93,22 +93,18 @@ <option value="history">Use a genome from the history</option> </param> <when value="cached"> - <repeat min="1" name="input_bams" title="BAM file"> - <param format="bam" label="BAM file" name="input_bam" type="data"> - <validator type="unspecified_build" /> - <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> - </param> - </repeat> + <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> + </param> <param label="Using reference genome" name="ref_file" type="select"> <options from_data_table="fasta_indexes" /> </param> </when> <when value="history"> - <repeat min="1" name="input_bams" title="BAM file"> - <param format="bam" label="BAM file" name="input_bam" type="data"> - <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> - </param> - </repeat> + <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True"> + <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> + </param> <param format="fasta" label="Using reference genome" name="ref_file" type="data" /> </when> </conditional> @@ -153,7 +149,7 @@ </when> <when value="do_not_perform_indel_calling" /> </conditional> - + </when> <when value="do_not_perform_genotype_likelihood_computation"> <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/> @@ -288,7 +284,7 @@ <![CDATA[ **What it does** -Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. +Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. ------ |