bwa_0_7_10: bwa-mem.xml comparison

comparison bwa-mem.xml @ 5:86c73f0eb389 draft default tip

Uploaded

author	devteam
date	Thu, 06 Nov 2014 14:52:29 -0500
parents	5e72d136a39e
children

comparison

equal deleted inserted replaced

-:d04dfa7de2dc
+:86c73f0eb389
 <?xml version="1.0"?>
-<tool id="bwa_mem_0_7_10" name="BWA-MEM" version="bwa-0.7.10-r837-dirty_galaxy_0.1">
+<tool id="bwa_mem_0_7_10" name="BWA-MEM" version="bwa-0.7.10-r837-dirty_galaxy_0.2">
+<macros>
+<import>bwa_macros.xml</import>
+</macros>
 <requirements>
 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
 <requirement type="package" version="1.1">samtools</requirement>
 </requirements>
 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
 -t "\${GALAXY_SLOTS:-1}"
 -v 1                                                                                      ## Verbosity is set to 1 (errors only)
 #if str( $fastq_input.fastq_input_selector ) == "paired_iv":                              ## For interleaved fastq files set -p option
 -p
-#if str( $fastq_input.iv_stats.iv_stats_selector ) == "True":                           ## check that insert statistics is used
+#if str( $fastq_input.iset_stats ):                                                     ## check that insert statistics is used
--I "${fastq_input.iv_stats.iset_stats}"
+-I "${fastq_input.iset_stats}"
 #end if
 #end if
 #if str( $analysis_type.analysis_type_selector ) == "pacbio":
 -x
 -R "@RG\tID:$rg.ID\tSM:$rg.SM"
 #end if
 #if str( $fastq_input.fastq_input_selector ) == "paired":
-#if str( $fastq_input.paired_stats.paired_stats_selector ) == "True":                   ## check that insert statistics is used
+#if str( $fastq_input.iset_stats ):                   ## check that insert statistics is used
--I "${fastq_input.paired_stats.iset_stats}"
+-I "${fastq_input.iset_stats}"
 #end if
 "${reference_fasta_filename}"
 "${fastq_input.fastq_input1}" "${fastq_input.fastq_input2}"
+#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
+#if str( $fastq_input.iset_stats ):                   ## check that insert statistics is used
+-I "${fastq_input.iset_stats}"
+#end if
+"${reference_fasta_filename}"
+"${fastq_input.fastq_input1.forward}" "${fastq_input.fastq_input1.reverse}"
 #else:
 "${reference_fasta_filename}"
 "${fastq_input.fastq_input1}"
 #end if
-| samtools view -Sb - > $bam_output
+| samtools view -Sb - > temporary_bam_file.bam &amp;&amp;
+samtools sort -f temporary_bam_file.bam ${bam_output}
 </command>
 <inputs>
 </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 folloing dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
+<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>
 <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>
 <option value="single">Single</option>
+<option value="paired_collection">Paired Collection</option>
 <option value="paired_iv">Paired Interleaved</option>
 </param>
 <when value="paired">
 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+<param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
-<!-- PE stat selection block 1: If you make any changes in this conditional block, copy them to PE stat selection block 2 below as well -->
+<sanitizer invalid_char="">
+<valid initial="string.digits"><add value=","/> </valid>
-<conditional name="paired_stats">
+</sanitizer>
-<param name="paired_stats_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Specify insert size statistics?" help="-I; if you choose to not specify, it will be inferred from the data"/>
+</param>
-<when value="set">
-<param name="iset_stats" type="text" value="250" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths in the form mean,sd,min,max" help="-I; only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
-<sanitizer invalid_char="">
-<valid initial="string.digits"><add value=","/> </valid>
-</sanitizer>
-</param>
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</conditional>
-<!-- end of PE stat selection block 1 -->
 </when>
 <when value="single">
 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
 </when>
+<when value="paired_collection">
+<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"/>
+<param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+<sanitizer invalid_char="">
+<valid initial="string.digits"><add value=","/> </valid>
+</sanitizer>
+</param>
+</when>
 <when value="paired_iv">
 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+<param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
-<!-- PE stat selection block 2: If you make any changes in this conditional block, copy them to PE stat selection block 1 above as well -->
+<sanitizer invalid_char="">
+<valid initial="string.digits"><add value=","/> </valid>
-<conditional name="iv_stats">
+</sanitizer>
-<param name="iv_stats_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Specify insert size statistics?" help="-I; if you choose to not specify, it will be inferred from the data"/>
+</param>
-<when value="set">
-<param name="iset_stats" type="text" value="250" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths in the form mean,sd,min,max" help="-I; only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
-<sanitizer invalid_char="">
-<valid initial="string.digits"><add value=","/> </valid>
-</sanitizer>
-</param>
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</conditional>
-<!-- end of PE stat selection block 2 -->
 </when>
 </conditional>
 <conditional name="rg">
-<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"/>
+<param name="rg_selector" type="select" label="Set read groups information?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details">
+<option value="set">Set</option>
+<option value="do_not_set" selected="True">Do not set</option>
+</param>
 <when value="set">
 <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">
 <sanitizer invalid_char="">
 <valid initial="string.printable"/>
 </sanitizer>
 <when value="pacbio">
 <!-- do nothing. all magic happens within <command> tag -->
 </when>
 <when value="full">
 <conditional name="algorithmic_options">
-<param name="algorithmic_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e 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.">
+<option value="set">Set</option>
+<option value="do_not_set" selected="True">Do not set</option>
+</param>
 <when value="set">
 <param name="k" type="integer" value="19" label="minimum seed length" help="-k; default=19"/>
 <param name="w" type="integer" value="100" label="band width for banded alignment" help="-w; default=100"/>
 <param name="d" type="integer" value="100" label="off-diagonal X-dropoff" help="-d; default=100"/>
 <param name="r" type="float" value="1.5" label="look for internal seeds inside a seed longer than -k * THIS VALUE" help="-r; default=1.5"/>
 </when>
 <when value="do_not_set">
 <!-- do nothing -->
 </when>
 </conditional>
 <conditional name="scoring_options">
-<param name="scoring_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options." />
+<param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
+<option value="set">Set</option>
+<option value="do_not_set" selected="True">Do not set</option>
+</param>
 <when value="set">
 <param name="A" type="integer" value="1" label="score for a sequence match" help="-A; scales options -T, -d, -B, -O, -E, -L, and -U; default=1"/>
 <param name="B" type="integer" value="4" label="penalty for mismatch" help="-B; default=4"/>
 <param name="O" type="text" value="6,6" label="gap open penalty for deletions and insertions" help="-O; default=6,6">
 <sanitizer invalid_char="">
 </when>
 <when value="do_not_set">
 <!-- do nothing -->
 </when>
 </conditional>
 <conditional name="io_options">
-<param name="io_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options." />
+<param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
+<option value="set">Set</option>
+<option value="do_not_set" selected="True">Do not set</option>
+</param>
 <when value="set">
 <param name="T" type="integer" value="30" label="minimum score to output" help="-T; default=30"/>
 <param name="h" type="integer" value="5" label="if there are this many hits with score >80% of the max score, output all in XA tag" help="-h; default=5"/>
 <param name="a" type="boolean" truevalue="-a" falsevalue="" label="output all alignments for single-ends or unpaired paired-ends" help="-a"/>
 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="append FASTA/FASTQ comment to BAM output" help="-C"/>
 -I FLOAT[,FLOAT[,INT[,INT]]]
 specify the mean, standard deviation (10% of the mean if absent), max
 (4 sigma from the mean if absent) and min of the insert size distribution.
 FR orientation only. [inferred]
-------
+@dataset_collections@
-.. class:: warningmark
+@RG@
-**An important note on Read Groups**
+@info@
-One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do thid directly in BWA MEM interface using the
-**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.
-This allows you to combine BAM files from, for example, multiple BWA MEM runs into a single dataset. This significantly simplifies downstream processing as
-instead of dealing with multiple datasets you only have to handle only one. This is possible because the readgroup information allows you to identify
-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
-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.
------
-.. class:: infomark
-**More info**
-To obtain more information about BWA MEM and ask questions use these resources:
-1. https://biostar.usegalaxy.org/
-2. https://www.biostars.org/
-3. https://github.com/lh3/bwa
-4. http://bio-bwa.sourceforge.net/
 </help>
 <citations>
 <citation type="doi">10.1093/bioinformatics/btp324</citation>

Mercurial > repos > devteam > bwa_0_7_10

comparison bwa-mem.xml @ 5:86c73f0eb389 draft default tip