| Previous changeset 2:19fa4f8a6088 (2014-09-29) Next changeset 4:d04dfa7de2dc (2014-11-06) |
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bwa.xml |
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| diff -r 19fa4f8a6088 -r 6bfb657c8fe1 bwa.xml --- a/bwa.xml Mon Sep 29 16:41:05 2014 -0400 +++ b/bwa.xml Thu Nov 06 14:51:23 2014 -0500 |
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| b'@@ -1,5 +1,6 @@\n <?xml version="1.0"?>\n-<tool id="bwa_aln_0_7_10" name="BWA" version="bwa-0.7.10-r837-dirty_galaxy_0.1">\n+<tool id="bwa_aln_0_7_10" name="BWA" version="bwa-0.7.10-r837-dirty_galaxy_0.2">\n+ \n <requirements>\n <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>\n <requirement type="package" version="1.1">samtools</requirement>\n@@ -50,7 +51,7 @@\n \n ####### Fastq paired\n \n- #if str( $input_type.input_type_selector ) == "paired":\n+ #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection":\n \n bwa aln\n -t "\\${GALAXY_SLOTS:-1}"\n@@ -58,7 +59,13 @@\n @command_options@\n \n "${reference_fasta_filename}"\n- "${input_type.fastq_input1}"\n+ \n+ #if str( $input_type.input_type_selector ) == "paired_collection":\n+ "${input_type.fastq_input1.forward}"\n+ #else\n+ "${input_type.fastq_input1}"\n+ #end if\n+ \n > first.sai &&\n \n bwa aln\n@@ -67,7 +74,13 @@\n @command_options@\n \n "${reference_fasta_filename}"\n- "${input_type.fastq_input2}"\n+ \n+ #if str( $input_type.input_type_selector ) == "paired_collection":\n+ "${input_type.fastq_input1.reverse}"\n+ #else\n+ "${input_type.fastq_input2}"\n+ #end if\n+\n > second.sai &&\n \n bwa sampe\n@@ -83,7 +96,15 @@\n \n @read_group_options@\n \n- "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1}" "${input_type.fastq_input2}"\n+ #if str( $input_type.input_type_selector ) == "paired_collection":\n+ \n+ "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1.forward}" "${input_type.fastq_input1.reverse}"\n+ \n+ #else:\n+ \n+ "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1}" "${input_type.fastq_input2}"\n+ \n+ #end if\n \n ####### Fastq single\n \n@@ -178,11 +199,15 @@\n \n #end if\n \n- | samtools view -Sb - > $bam_output\n+ | samtools view -Sb - > temporary_bam_file.bam &&\n+ \n+ samtools sort -f temporary_bam_file.bam ${bam_output}\n+ \n \n </command>\n \n <macros>\n+ <import>bwa_macros.xml</import>\n <token name="@command_options@"> \n #if str( $analysis_type.analysis_type_selector ) == "illumina":\n \n@@ -226,7 +251,10 @@\n </token>\n \n <xml name="advanced_pe_options">\n- <param name="adv_pe_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set advanced paired end options?" help="Provides additional controls"/>\n+ <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?" help="Provides additional controls">\n+ <option value="set">Set</option>\n+ <option value="do_not_set" selected="True">Do not set</option>\n+ </param>\n <when value="set">\n <param name="a" type="integer" value="500" label="Maximum insert size for a read pair to be considered being mapped properly." help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/>\n <param name="o" type="integer" value="100000" label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read." help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/>\n@@ -238,8 +266,11 @@\n <!-- do nothing -->\n </when>\n </xml>\n- <xml name="advances_se_options">\n- <param name="adv_se_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set advanced single end options?" help="Provides additional controls"/>\n+ <xml name="advanced_se_options">\n+ <param name="adv_se_options_selector" type="select" label="Set advanced single end options?" help="Provides additional controls">\n+ '..b'option value="paired_bam">Paired BAM</option>\n <option value="single_bam">Single BAM</option>\n@@ -284,12 +316,23 @@\n <expand macro="advanced_pe_options" />\n \n </conditional>\n- </when> \n+ </when>\n+ \n+ <when value="paired_collection">\n+ <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>\n+ <conditional name="adv_pe_options">\n+ \n+ <expand macro="advanced_pe_options" />\n+ \n+ </conditional>\n+ </when>\n+ \n+ \n <when value="single">\n <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>\n <conditional name="adv_se_options">\n \n- <expand macro="advances_se_options" />\n+ <expand macro="advanced_se_options" />\n \n </conditional>\n </when>\n@@ -304,11 +347,12 @@\n \n </conditional>\n </when>\n+ \n <when value="single_bam">\n <param name="bam_input" type="data" format="bam" label="Select BAM dataset" help="Specify BAM dataset with single reads"/>\n <conditional name="adv_bam_se_options">\n \n- <expand macro="advances_se_options" />\n+ <expand macro="advanced_se_options" />\n \n </conditional>\n </when>\n@@ -316,7 +360,10 @@\n </conditional>\n \n <conditional name="rg">\n- <param name="rg_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Specify readgroup information?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details"/>\n+ <param name="rg_selector" type="select" label="Set readgroups information?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details">\n+ <option value="set">Set</option>\n+ <option value="do_not_set" selected="True">Do not set</option>\n+ </param>\n <when value="set">\n <param name="ID" type="text" value="readgroup1" size="20" label="Specify readgroup ID" help="This value must be unique among multiple samples in your experiment">\n <sanitizer invalid_char="">\n@@ -465,32 +512,12 @@\n -n INT maximum hits to output for paired reads [3]\n -r STR read group header line [null]\n \n-------\n \n-.. class:: warningmark\n-\n-**An important note on Read Groups**\n-\n-One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do thid directly in BWA interface using the\n-**Specify readgroup information?** widget. If you are not familiar with readgroups you shold know that this is effectively a way to tag reads with an additional ID.\n-This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as\n-instead of dealing with multiple datasets you only have to handle only one. This is possible because the readgroup information allows you to identify\n-data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller\n-present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file.\n+@dataset_collections@\n \n------\n-\n-.. class:: infomark\n-\n-**More info**\n+@RG@\n \n-To obtain more information about BWA and ask questions use these resources:\n-\n- 1. https://biostar.usegalaxy.org/\n- 2. https://www.biostars.org/\n- 3. https://github.com/lh3/bwa\n- 4. http://bio-bwa.sourceforge.net/\n- \n+@info@\n \n </help>\n <citations>\n' |