annotate macros.xml @ 2:9efbd847e5d1 draft default tip

"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"

<macros>
    <token name="@TOOL_VERSION@">1.3.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@online{fgbio,
              author = {Tim Fennell, Nils Homer},
              title = {fgbio},
              year = 2015,
              url = {https://github.com/fulcrumgenomics/fgbio},
              urldate = {2021-03-01}
            }</citation>
        </citations>
    </xml>
    <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
    <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
    <xml name="read_structures_validator" token_pattern="@READ_STRUCTURES_PATTERN@">
            <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
    </xml>
    <xml name="read_structures" token_pattern="@READ_STRUCTURES_PATTERN@">
        <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
            <expand macro="read_structures_validator" pattern="@READ_STRUCTURE_PATTERN@" />
        </param>
    </xml>

    <xml name="fastq_input" token_fastqtype="reads" token_defaultpaired="True" token_defaultnone="False">
        <conditional name="@FASTQTYPE@">
            <param name="type" type="select" label="Library type of FASTQ @FASTQTYPE@">
                <option value="none" selected="@DEFAULTNONE@">NO fastq @FASTQTYPE@</option>
                <option value="single">Single-end</option>
                <option value="paired" selected="@DEFAULTPAIRED@">Paired-end</option>
                <option value="paired_collection">Paired-end Dataset Collection</option>
            </param>
            <when value="none"/>
            <when value="single">
                <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
                <expand macro="read_structures" pattern="@READ_STRUCTURE_PATTERN@" />
            </when>
            <when value="paired">
                <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads #1 in FASTQ format" />
                <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads #2 in FASTQ format" />
                <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
            </when>
            <when value="paired_collection">
                <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired Reads in FASTQ format" />
                <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
            </when>
        </conditional>
    </xml>
    <xml name="fastq_reads">
        <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
    </xml>
    <xml name="fastq_inputs">
        <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
        <expand macro="fastq_input" fastqtype="indices" defaultpaired="False" defaultnone="True"/>
    </xml>
    <token name="@FASTQ_READS@"><![CDATA[
        #set $fastqs = []
        #set $read_structs = []
        #if $reads.type == 'single':
            $fastqs.append($reads.input_single)
        #elif $reads.type == 'paired':
            $fastqs.append($reads.input_read1)
            $fastqs.append($reads.input_read2)
        #elif $reads.type == 'paired_collection':
            $fastqs.append($reads.input_readpair.forward)
            $fastqs.append($reads.input_readpair.reverse)
        #end if
        #if $reads.type !='none' and $reads.read_structures:
            $read_structs.append(str($reads.read_structures))
        #end if
        #set $read_structures = "%s" % (' '.join($read_structs))
        #if $read_structs:
            --read-structures $read_structures
        #end if
]]></token>
    <token name="@LINK_FASTQ_INPUTS@"><![CDATA[
#import re
#def identifier_or_name($input1)
    #if hasattr($input1, 'element_identifier')
        #return $input1.element_identifier
    #else
        #return $input1.name
    #end if
#end def
#def clean($name1)
    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fq|fastq)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
    #return $name_clean
#end def
#def ln_name($ds)
    #set $ext = ''
    #if $ds.is_of_type('mzml') or $ds.is_of_type('fastq.gz')
        #set $ext = ".fastq.gz"
    #else if $ds.is_of_type('fastq')
        #set $ext = ".fastq"
    #end if
    #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
    #return $name
#end def
        #set $fastqs = []
        #set $read_structs = []
        #if $reads.type == 'single':
            #set $i_name = $ln_name($reads.input_single)
            #silent $fastqs.append($i_name)
            ln -s '$reads.input_single' '$i_name' &&
        #elif $reads.type == 'paired':
            #set $f_name = $ln_name($reads.input_read1)
            #silent $fastqs.append($f_name)
            ln -s '$reads.input_read1' '$f_name' &&
            #set $r_name = $ln_name($reads.input_read2)
            #silent $fastqs.append($r_name)
            ln -s '$reads.input_read2' '$r_name' &&
        #elif $reads.type == 'paired_collection':
            #set $f_name = $ln_name($reads.input_readpair.forward)
            #silent $fastqs.append($f_name)
            ln -s '$reads.input_readpair.forward' '$f_name' &&
            #set $r_name = $ln_name($reads.input_readpair.reverse)
            #silent $fastqs.append($r_name)
            ln -s '$reads.input_readpair.reverse' '$r_name' &&
        #end if
        #if $reads.type !='none' and $reads.read_structures:
            $read_structs.append(str($reads.read_structures))
        #end if
        #if $indices.type == 'single':
            #set $i_name = $ln_name($indices.input_single)
            #silent $fastqs.append($i_name)
            ln -s '$indices.input_single' '$i_name' &&
        #elif $indices.type == 'paired':
            #set $f_name = $ln_name($indices.input_read1)
            #silent $fastqs.append($f_name)
            ln -s '$indices.input_read1' '$f_name' &&
            #set $r_name = $ln_name($indices.input_read2)
            #silent $fastqs.append($r_name)
            ln -s '$indices.input_read2' '$r_name' &&
        #elif $indices.type == 'paired_collection':
            #set $f_name = $ln_name($indices.input_readpair.forward)
            #silent $fastqs.append($f_name)
            ln -s '$indices.input_readpair.forward' '$f_name' &&
            #set $r_name = $ln_name($indices.input_readpair.reverse)
            #silent $fastqs.append($r_name)
            ln -s '$indices.input_readpair.reverse' '$r_name' &&
        #end if
        #if $indices.type != 'none' and $indices.read_structures:
            $read_structs.append(str($indices.read_structures))
        #end if
]]></token>
    <token name="@FASTQ_INPUTS@"><![CDATA[
        --input 
        #for $input in $fastqs
            '$input'
        #end for
        #set $read_structures = "%s" % (' '.join($read_structs))
        #if $read_structs:
            --read-structures $read_structures
        #end if
]]></token>
        <xml name="inherit_format_1">
            <actions>
                <conditional name="library.type">
                    <when value="single">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </xml>

        <xml name="inherit_format_2">
            <actions>
                <conditional name="library.type">
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="library.input_2" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </xml>
    <xml name="sam_tag_validator">

            <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
    </xml>
    <xml name="sam_sort_order">
        <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
            <option value="TemplateCoordinate">TemplateCoordinate</option>
            <option value="Coordinate">Coordinate</option>
            <option value="Queryname">Queryname</option>
            <option value="Random">Random</option>
            <option value="RandomQuery">RandomQuery</option>
        </param>
    </xml>
    
    <xml name="sort_order_change_format">
        <change_format>
            <when input="sort_order" value="Coordinate" format="bam" />
            <when input="sort_order" value="TemplateCoordinate" format="bam" />
            <when input="sort_order" value="QueryName" format="unsorted.bam" />
            <when input="sort_order" value="Random" format="unsorted.bam" />
            <when input="sort_order" value="RandomQuery" format="unsorted.bam" />
        </change_format>
    </xml>

    <token name="@READ_STRUCTURES_HELP@"><![CDATA[
**Read Structures**

Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:

 -  T identifies a template read
 -  B identifies a sample barcode read
 -  M identifies a unique molecular index read
 -  S identifies a set of bases that should be skipped or ignored

The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:

:: 

    --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B

Alternative if you know your reads are of fixed length you could specify:

:: 

    --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B


]]></token>
    <xml name="citations">
        <citations>
            <yield />
        </citations>
    </xml>
</macros>