annotate bismark_bowtie_wrapper.xml @ 4:427fb56f2e41 draft default tip

- new options - fixes

<tool id="bismark_bowtie" name="Bismark" version="0.7.7.3">
    <!-- Wrapper compatible with Bismark version 0.7.7 -->
    <description>bisulfite mapper (bowtie)</description>
    <!--<version_command>bismark version</version_command>-->
    <requirements>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
        <requirement type="package" version="0.12.8">bowtie</requirement>
        <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
    </requirements>
    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_wrapper.py

        --bismark_path \$SCRIPT_PATH

        ##
        ## Bismark Genome Preparation, if desired.
        ##

        ## Handle reference file.
        #if $refGenomeSource.genomeSource == "history":
            --own-file=$refGenomeSource.ownFile
        #else:
            --indexes-path ${refGenomeSource.index.fields.path}
        #end if


        ##
        ##  Input parameters
        ##


        #if $singlePaired.sPaired == "single":
            --single-paired $singlePaired.input_singles

            #if $singlePaired.input_singles.ext == "fastqillumina":
                --phred64-quals
                --fastq
            #elif $singlePaired.input_singles.ext == "fastqsanger":
                --fastq
            #elif $singlePaired.input_singles.ext == "fasta":
                --fasta
            #end if
        #else:
            --mate-paired
            #set $mate1 = list()
            #set $mate2 = list()
            #for $mate_pair in $singlePaired.mate_list
                $mate1.append( str($mate_pair.input_mate1) )
                $mate2.append( str($mate_pair.input_mate2) )
            #end for

            --mate1 #echo ','.join($mate1)
            --mate2 #echo ','.join($mate2)

            #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
                --phred64-quals
                --fastq
            #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
                --fastq
            #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
                --fasta
            #end if

            -I $singlePaired.minInsert
            -X $singlePaired.maxInsert
        #end if


        ## for now hardcode the value for the required memory per thread in --best mode
        --chunkmbs 512


        #if $params.settingsType == "custom":

            ## default 20
            --seed-len $params.seed_len
            ## default 0
            --seed-mismatches $params.seed_mismatches

            ## default 70
            ##--maqerr $params.maqerr

            ## default unlimited
            #if $params.qupto != 0:
                --qupto $params.qupto
            #end if
            #if $params.skip_reads != 0:
                --skip-reads $params.skip_reads
            #end if

            ###if str($params.isReportOutput) == "yes":
            ##    --output-report-file $report_file
            ###end if

        #end if

        ##
        ## Output parameters.
        ##
        --output $output
        $suppress_header

      #if str( $singlePaired.sPaired ) == "single"
        #if $output_unmapped_reads_l
          --output-unmapped-reads $output_unmapped_reads_l
        #end if
        #if $output_suppressed_reads_l
          --output-suppressed-reads $output_suppressed_reads_l
        #end if
      #else
        #if $output_unmapped_reads_l and $output_unmapped_reads_r
          --output-unmapped-reads-l $output_unmapped_reads_l
          --output-unmapped-reads-r $output_unmapped_reads_r
        #end if
        #if $output_suppressed_reads_l and $output_suppressed_reads_l
          --output-suppressed-reads-l $output_suppressed_reads_l
          --output-suppressed-reads-r $output_suppressed_reads_r
        #end if
      #end if

    </command>
    <inputs>
        <conditional name="refGenomeSource">
          <param name="genomeSource" 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">
            <option value="indexed">Use a built-in index</option>
            <option value="history">Use one from the history</option>
          </param>
          <when value="indexed">
            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
              <options from_data_table="bowtie_indexes">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
              </options>
            </param>
          </when>  <!-- build-in -->
          <when value="history">
            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
          </when>  <!-- history -->
        </conditional>  <!-- refGenomeSource -->

        <!-- Input Parameters -->
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library mate-paired?">
              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
            </when>
            <when value="paired">
                <repeat name="mate_list" title="Paired End Pairs" min="1">
                    <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
                    <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
                </repeat>
                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
            </when>
        </conditional>


        <conditional name="params">
            <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
              <option value="default">Use Defaults</option>
              <option value="custom">Full parameter list</option>
            </param>
            <when value="default" />
            <!-- Full/advanced params. -->
            <when value="custom">
                <!-- -n -->
                <param name="seed_mismatches" type="select" label="The maximum number of mismatches permitted in the 'seed'.">
                    <option value="0">0</option>
                    <option value="1">1</option>
                    <option value="2" selected="true">2</option>
                    <option value="3">3</option>
                </param>
                <!-- -l -->
                <param name="seed_len" type="integer" value="28" label="The 'seed length'; The number of bases of the high quality end of the read to which the maximum number of mismatches applies." />
                <!--
                <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
                -->
                <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
                <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />

                <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
                <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" />
                <!-- output Options -->
                <!-- 
                <param name="isReportOutput" type="select" label="Offer all report files concatenated in one file.">
                    <option value="yes">yes</option>
                    <option value="no">no</option>
                </param>
                -->
                <!--end output options --> 
            </when>  <!-- full -->
      </conditional>  <!-- params -->
      <param name="suppress_header" type="boolean" truevalue="--suppress-header" falsevalue="" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
    </inputs>
    <outputs>
        <!-- that does not work
        <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
            <filter>str($params.isReportOutput) == "yes"</filter>
        </data>
        -->
        <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
          <actions>
            <conditional name="refGenomeSource.genomeSource">
              <when value="indexed">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
                    <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                    <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                  </option>
                </action>
              </when>
              <when value="history">
                <action type="metadata" name="dbkey">
                  <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
                </action>
              </when>
            </conditional>
          </actions>
        </data>

    <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
      <filter>
        ((
          params['settingsType'] == "custom" and
          params['suppressed_read_file'] is True
        ))
      </filter>
      <actions>
        <conditional name="singlePaired.sPaired">
          <when value="single">
            <action type="format">
              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
            </action>
          </when>
          <when value="paired">
            <action type="format">
              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>

    <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
      <filter>singlePaired['sPaired'] == "paired"</filter>
      <filter>params['settingsType'] == "custom"</filter>
      <filter>params['supressed_read_file'] is True</filter>
      <actions>
        <conditional name="singlePaired.sPaired">
          <when value="single">
            <action type="format">
              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
            </action>
          </when>
          <when value="paired">
            <action type="format">
              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>

    <!-- Outout unmapped reads -->
    <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
      <filter>
        ((
          params['settingsType'] == "custom" and
          params['unmapped_read_file'] is True
        ))
      </filter>
      <actions>
        <conditional name="singlePaired.sPaired">
          <when value="single">
            <action type="format">
              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
            </action>
          </when>
          <when value="paired">
            <action type="format">
              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
      <filter>singlePaired['sPaired'] == "paired"</filter>
      <filter>params['settingsType'] == "custom"</filter>
      <filter>params['unmapped_read_file'] is True</filter>
      <actions>
        <conditional name="singlePaired.sPaired">
          <when value="single">
            <action type="format">
              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
            </action>
          </when>
          <when value="paired">
            <action type="format">
              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
        
        
    </outputs>

    <tests>
    </tests>

    <help>

**What it does**

Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
(C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
sequence from the genome and determine if there were any protected C's present or not.

.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
re-enabled by using non_directional mode.

It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.

------

**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/


.. class:: warningmark

Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.

------

**Input formats**

Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.

------

**A Note on Built-in Reference Genomes**

The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.

------

The final output of Bismark is in SAM format by default.

**Outputs**

The output is in SAM format, and has the following columns::

    Column  Description
  --------  --------------------------------------------------------
  1  QNAME  seq-ID
  2  FLAG   this flag tries to take the strand a bisulfite read 
            originated from into account 
            (this is different from ordinary DNA alignment flags!)
  3  RNAME  chromosome
  4  POS    start position
  5  MAPQ   always 255
  6  CIGAR  extended CIGAR string
  7  MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
  8  MPOS   1-based Mate POSition
  9  ISIZE  Inferred insert SIZE
  10 SEQ    query SEQuence on the same strand as the reference
  11 QUAL   Phred33 scale
  12 NM-tag edit distance to the reference)
  13 XX-tag base-by-base mismatches to the reference. 
            This does not include indels.
  14 XM-tag methylation call string
  15 XR-tag read conversion state for the alignment
  16 XG-tag genome conversion state for the alignment
  

Each read of paired-end alignments is written out in a separate line in the above format.


It looks like this (scroll sideways to see the entire example)::

  QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
  HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
  HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh

-------

**Bismark settings**

All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.

------

**Bismark parameter list**

This is an exhaustive list of Bismark options.

Input::

  --singles              A comma- or space-separated list of files containing the reads to be aligned (e.g.
                         lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
                         produce one mapping result and one report file per input file.

  -1 mates1              Comma-separated list of files containing the #1 mates (filename usually includes
                         "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
                         correspond file-for-file and read-for-read with those specified in mates2.
                         Reads may be a mix of different lengths. Bismark will produce one mapping result
                         and one report file per paired-end input file pair.

  -2 mates2              Comma-separated list of files containing the #2 mates (filename usually includes
                         "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
                         correspond file-for-file and read-for-read with those specified in mates1.
                         Reads may be a mix of different lengths.

  -q/--fastq             The query input files (specified as mate1,mate2 or singles are FASTQ
                         files (usually having extension .fg or .fastq). This is the default. See also
                         --solexa-quals.

  -f/--fasta             The query input files (specified as mate1,mate2 or singles are FASTA
                         files (usually havin extension .fa, .mfa, .fna or similar). All quality values
                         are assumed to be 40 on the Phred scale.

  -s/--skip INT          Skip (i.e. do not align) the first INT reads or read pairs from the input.

  -u/--upto INT          Only aligns the first INT reads or read pairs from the input. Default: no limit.

  --phred33-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.

  --phred64-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.

  --solexa-quals         Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
                         (which can't). The formula for conversion is: 
                         phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
                         is usually the right option for use with (unconverted) reads emitted by the GA
                         Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.

  --solexa1.3-quals      Same as --phred64-quals. This is usually the right option for use with (unconverted)
                         reads emitted by GA Pipeline version 1.3 or later. Default: off.


Alignment::

  -n/--seedmms INT       The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
                         of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 
                         default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).

  -l/--seedlen           The "seed length"; i.e., the number of bases of the high quality end of the read to
                         which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
                         larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).

  -e/--maqerr INT        Maximum permitted total of quality values at all mismatched read positions throughout
                         the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
                         quality values to the nearest 10 and saturates at 30. This value is not relevant for
                         Bowtie 2.

  --chunkmbs INT         The number of megabytes of memory a given thread is given to store path descriptors in
                         --best mode. Best-first search must keep track of many paths at once to ensure it is
                         always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
                         memory impact of the descriptors, but they can still grow very large in some cases. If
                         you receive an error message saying that chunk memory has been exhausted in --best mode,
                         try adjusting this parameter up to dedicate more memory to the descriptors. This value
                         is not relevant for Bowtie 2. Default: 512.

  -I/--minins INT        The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
                         a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
                         with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
                         satisfied). A 19-bp gap would not be valid in that case. Default: 0.

  -X/--maxins INT        The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
                         a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
                         60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
                         A 61-bp gap would not be valid in that case. Default: 500.



Output::

  --non_directional      The sequencing library was constructed in a non strand-specific manner, alignments to all four
                         bisulfite strands will be reported. Default: OFF.

                         (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
                         to the original strands are merely theoretical and should not exist in reality. Specifying directional
                         alignments (which is the default) will only run 2 alignment threads to the original top (OT)
                         or bottom (OB) strands in parallel and report these alignments. This is the recommended option
                         for sprand-specific libraries).

  --sam-no-hd            Suppress SAM header lines (starting with @). This might be useful when very large input files are
                         split up into several smaller files to run concurrently and the output files are to be merged.

  --quiet                Print nothing besides alignments.

  --vanilla              Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
                         of SAM format output.

  -un/--unmapped         Write all reads that could not be aligned to a file in the output directory. Written reads will
                         appear as they did in the input, without any translation of quality values that may have
                         taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
                         and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
                         with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
                         are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.

  --ambiguous            Write all reads which produce more than one valid alignment with the same number of lowest
                         mismatches or other reads that fail to align uniquely to a file in the output directory.
                         Written reads will appear as they did in the input, without any of the translation of quality
                         values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
                         parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
                         _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.

  -o/--output_dir DIR    Write all output files into this directory. By default the output files will be written into
                         the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
                         to create it first. The path to the output folder can be either relative or absolute.

  --temp_dir DIR          Write temporary files to this directory instead of into the same directory as the input files. If
                         the specified folder does not exist, Bismark will attempt to create it first. The path to the
                         temporary folder can be either relative or absolute.

  </help>
</tool>