Mercurial > repos > devteam > bwa
diff bwa-mem.xml @ 2:b4dfb5470bf3 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author | devteam |
---|---|
date | Fri, 30 Dec 2016 08:10:56 -0500 |
parents | 8955a9521def |
children | 0bde88ff668c |
line wrap: on
line diff
--- a/bwa-mem.xml Fri Dec 18 18:51:08 2015 -0500 +++ b/bwa-mem.xml Fri Dec 30 08:10:56 2016 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bwa_mem" name="Map with BWA-MEM" version="0.4.2"> +<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.1"> <description>- map medium and long reads (> 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -8,44 +8,8 @@ <expand macro="requirements" /> <expand macro="stdio" /> <command> - #set $reference_fasta_filename = "localref.fa" - - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - - ## The following shell commands decide with of the BWA indexing algorithms (IS or BWTSW) will be run - ## depending ob the size of the input FASTA dataset - ( - size=`stat -c %s "${reference_fasta_filename}" 2>/dev/null`; ## Linux - if [ $? -eq 0 ]; - then - if [ "\$size" -lt 2000000000 ]; - then - bwa index -a is "${reference_fasta_filename}"; - echo "Generating BWA index with is algorithm"; - else - bwa index -a bwtsw "${reference_fasta_filename}"; - echo "Generating BWA index with bwtsw algorithm"; - fi; - fi; - - eval \$(stat -s "${reference_fasta_filename}" 2>/dev/null); ## OSX - if [ -n "\$st_size" ]; - then - if [ "\$st_size" -lt 2000000000 ]; - then - bwa index -a is "${reference_fasta_filename}"; - echo "Generating BWA index with is algorithm"; - else - bwa index -a bwtsw "${reference_fasta_filename}"; - echo "Generating BWA index with bwtsw algorithm"; - fi; - fi; - ) && - - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if +<![CDATA[ + @set_reference_fasta_filename@ ## Begin BWA-MEM command line @@ -62,6 +26,10 @@ #if str( $analysis_type.analysis_type_selector ) == "pacbio": -x pacbio + #elif str( $analysis_type.analysis_type_selector ) == "ont2d": + -x ont2d + #elif str( $analysis_type.analysis_type_selector ) == "intractg": + -x intractg #elif str( $analysis_type.analysis_type_selector ) == "full": #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set": ## Algorithmic options -k "${analysis_type.algorithmic_options.k}" @@ -132,31 +100,12 @@ "${fastq_input.fastq_input1}" #end if - | samtools view -Sb - > temporary_bam_file.bam && - - samtools sort -f temporary_bam_file.bam ${bam_output} + | samtools sort -O bam -o '$bam_output' +]]> </command> <inputs> - - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> - <option value="cached">Use a built-in genome index</option> - <option value="history">Use a genome from history and build index</option> - </param> - <when value="cached"> - <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> - <options from_data_table="bwa_mem_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - </when> - <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> - </when> - </conditional> + <expand macro="reference_source_conditional" /> <conditional name="fastq_input"> <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> <option value="paired">Paired</option> @@ -200,7 +149,9 @@ <param name="analysis_type_selector" type="select" label="Select analysis mode"> <option value="illumina">1.Simple Illumina mode</option> <option value="pacbio">2.PacBio mode (-x pacbio)</option> - <option value="full">3.Full list of options</option> + <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option> + <option value="intractg">4.Intra-species contigs mode (-x intractg)</option> + <option value="full">5.Full list of options</option> </param> <when value="illumina"> <!-- do nothing --> @@ -208,6 +159,12 @@ <when value="pacbio"> <!-- do nothing. all magic happens within <command> tag --> </when> + <when value="ont2d"> + <!-- do nothing. all magic happens within <command> tag --> + </when> + <when value="intractg"> + <!-- do nothing. all magic happens within <command> tag --> + </when> <when value="full"> <conditional name="algorithmic_options"> <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options."> @@ -304,6 +261,7 @@ <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="index_a" value="is"/> <param name="fastq_input_selector" value="paired"/> <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>