comparison samtools_view.xml @ 1:6ade12d94f9a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3

0:00d1f08bdcdc

        ## additional reference data
        #if $reffa!=None:
            -T '$reffa'
            -t '$reffai'
        #else:
            --output-fmt-option no_ref
        #end if

        infile
        

            </when>
            <when value="no"/>
        </conditional>
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Reference data">
		    <help>Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).</help>
                <option value="no" selected="True">No, see help (-output-fmt-option no_ref)</option>
		<option value="history">Use a genome/index from the history (-t/-T)</option>
		<option value="cached">Use a built-in genome (-t/-T)</option>
            </param>
            <when value="no"/>
            <when value="history">
                <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
            </when>

Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type". 

.. class:: infomark 

samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed. 
CRAM is (primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM. But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM). 

The Galaxy tool allows both possibilities using the "reference data" option:

- the default ("no reference") 
- reference data can be chosen from history or built in genomes can be used

The reference data required for reading/writing reference based CRAM.

**Filtering alignments**

samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments. 

1:6ade12d94f9a

        ## additional reference data
        #if $reffa!=None:
            -T '$reffa'
            -t '$reffai'
        #end if

        ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
        #if $outtype=='cram':
            --output-fmt-option no_ref
        #end if

        infile
        

            </when>
            <when value="no"/>
        </conditional>
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Reference data">
                <help>Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).</help>
                <option value="no" selected="True">No, see help (-output-fmt-option no_ref)</option>
                <option value="history">Use a genome/index from the history (-t/-T)</option>
                <option value="cached">Use a built-in genome (-t/-T)</option>
            </param>
            <when value="no"/>
            <when value="history">
                <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
            </when>

Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type". 

.. class:: infomark 

samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed. 
CRAM is (intended as a primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM. 
But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM). 

The Galaxy tool **currently generates only CRAM without reference sequence**.

For reference based CRAM input the correct refernce sequence needs to be specified.

**Filtering alignments**

samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments.