Mercurial > repos > jjohnson > fgbio_fastq_to_bam
changeset 2:6137ff37bea1 draft default tip
"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
| author | jjohnson |
|---|---|
| date | Thu, 19 Aug 2021 15:11:08 +0000 |
| parents | 4635a93ebd91 |
| children | |
| files | fgbio_fastq_to_bam.xml macros.xml macros.xml.bak |
| diffstat | 3 files changed, 194 insertions(+), 69 deletions(-) [+] |
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--- a/fgbio_fastq_to_bam.xml Wed Feb 24 13:01:53 2021 +0000 +++ b/fgbio_fastq_to_bam.xml Thu Aug 19 15:11:08 2021 +0000 @@ -6,16 +6,11 @@ <expand macro="requirements" /> <version_command>fgbio --version</version_command> <command detect_errors="exit_code"><![CDATA[ + @LINK_FASTQ_INPUTS@ fgbio FastqToBam - --input - #for $input in $inputs - '$input' - #end for + @FASTQ_INPUTS@ --sample='$sample' --library='$library' - #if $read_structures: - --read-structures $read_structures - #end if --sort='$sort' --output '$output' ## optional bam header content @@ -51,13 +46,12 @@ #end if ]]></command> <inputs> - <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/> + <expand macro="fastq_inputs"/> <param argument="--sample" type="text" value="" label="The name of the sequenced sample"> + <validator type="empty_field"/> </param> <param argument="--library" type="text" value="" label="The name/ID of the sequenced library"> - </param> - <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ"> - <expand macro="read_structures_validator" /> + <validator type="empty_field"/> </param> <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname" help="If true, queryname sort the BAM file, otherwise preserve input order."/>
--- a/macros.xml Wed Feb 24 13:01:53 2021 +0000 +++ b/macros.xml Thu Aug 19 15:11:08 2021 +0000 @@ -1,18 +1,205 @@ <macros> <token name="@TOOL_VERSION@">1.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement> <yield/> </requirements> </xml> + <xml name="citations"> + <citations> + <citation type="bibtex">@online{fgbio, + author = {Tim Fennell, Nils Homer}, + title = {fgbio}, + year = 2015, + url = {https://github.com/fulcrumgenomics/fgbio}, + urldate = {2021-03-01} + }</citation> + </citations> + </xml> <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token> <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token> - <xml name="read_structures_validator"> + <xml name="read_structures_validator" token_pattern="@READ_STRUCTURES_PATTERN@"> <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</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">
--- a/macros.xml.bak Wed Feb 24 13:01:53 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -<macros> - <token name="@TOOL_VERSION@">1.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement> - <yield/> - </requirements> - </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"> - <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator> - </xml> - <xml name="sam_tag_validator"> - <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator> - </xml> - <xml name="sam_sort_order"> - <param argument="--sort-order" type="select" optional="true" label="Sort BAM by"> - <option value="Coordinate">Coordinate</option> - <option value="Queryname">Queryname</option> - <option value="Random">Random</option> - <option value="RandomQuery">RandomQuery</option> - </param> - </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>