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Commit message:
"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08" |
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fgbio_sort_fastq.xml macros.xml |
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| diff -r 000000000000 -r 099a35a39c29 fgbio_sort_fastq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fgbio_sort_fastq.xml Thu Aug 19 15:13:55 2021 +0000 |
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| @@ -0,0 +1,33 @@ +<tool id="fgbio_sort_fastq" name="fgbio SortFastq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description>Sorts the records in a FASTQ file based on the lexicographic ordering of their read names</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>fgbio --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + fgbio SortFastq + --input '$input' + #if $input.is_of_type("fastq.gz", "fastqsanger.gz") + --output output.fastq.gz + && cp output.fastq.gz '$output' + #else + --output output.fastq + && cp output.fastq '$output' + #end if + ]]></command> + <inputs> + <param name="input" type="data" format="fastq,fastq.gz" label="fastq file to be sorted"/> + </inputs> + <outputs> + <data name="output" format_source="input" label="Sorted ${input.name}"/> + </outputs> + <help><![CDATA[ +**fgbio SortFastq** + +Sorts a FASTQ file. Sorts the records in a FASTQ file based on the lexicographic ordering of their read names. Input and output files can be either uncompressed or gzip-compressed. + +http://fulcrumgenomics.github.io/fgbio/tools/latest/SortFastq.html + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 099a35a39c29 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Aug 19 15:13:55 2021 +0000 |
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| b'@@ -0,0 +1,254 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">1.3.0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="bibtex">@online{fgbio,\n+ author = {Tim Fennell, Nils Homer},\n+ title = {fgbio},\n+ year = 2015,\n+ url = {https://github.com/fulcrumgenomics/fgbio},\n+ urldate = {2021-03-01}\n+ }</citation>\n+ </citations>\n+ </xml>\n+ <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>\n+ <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\\s@READ_STRUCTURE_PATTERN@)*</token>\n+ <xml name="read_structures_validator" token_pattern="@READ_STRUCTURES_PATTERN@">\n+ <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>\n+ </xml>\n+ <xml name="read_structures" token_pattern="@READ_STRUCTURES_PATTERN@">\n+ <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">\n+ <expand macro="read_structures_validator" pattern="@READ_STRUCTURE_PATTERN@" />\n+ </param>\n+ </xml>\n+\n+ <xml name="fastq_input" token_fastqtype="reads" token_defaultpaired="True" token_defaultnone="False">\n+ <conditional name="@FASTQTYPE@">\n+ <param name="type" type="select" label="Library type of FASTQ @FASTQTYPE@">\n+ <option value="none" selected="@DEFAULTNONE@">NO fastq @FASTQTYPE@</option>\n+ <option value="single">Single-end</option>\n+ <option value="paired" selected="@DEFAULTPAIRED@">Paired-end</option>\n+ <option value="paired_collection">Paired-end Dataset Collection</option>\n+ </param>\n+ <when value="none"/>\n+ <when value="single">\n+ <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n+ <expand macro="read_structures" pattern="@READ_STRUCTURE_PATTERN@" />\n+ </when>\n+ <when value="paired">\n+ <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads #1 in FASTQ format" />\n+ <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads #2 in FASTQ format" />\n+ <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />\n+ </when>\n+ <when value="paired_collection">\n+ <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired Reads in FASTQ format" />\n+ <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="fastq_reads">\n+ <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>\n+ </xml>\n+ <xml name="fastq_inputs">\n+ <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>\n+ <expand macro="fastq_input" fastqtype="indices" defaultpaired="False" defaultnone="True"/>\n+ </xml>\n+ <token name="@FASTQ_READS@"><![CDATA[\n+ #set $fastqs = []\n+ #set $read_structs = []\n+ #if $reads.type == \'single\':\n+ $fastqs.append($reads.input_single)\n+ #elif $reads.type == \'paired\':\n+ $fastqs.append($reads.input_read1)\n+ $fastqs.append($reads.input_read2)\n+ #elif $reads.type == \'paired_collection\':\n+ $fastqs.append($reads.input_readpair.forward)\n+ $fastqs.append($reads.input_readpair.reverse)\n+ #end if\n+ #if $reads.type !=\'none\' and $reads.read_structures:\n+ $read'..b'-read-structures $read_structures\n+ #end if\n+]]></token>\n+ <xml name="inherit_format_1">\n+ <actions>\n+ <conditional name="library.type">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </xml>\n+\n+ <xml name="inherit_format_2">\n+ <actions>\n+ <conditional name="library.type">\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_2" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </xml>\n+ <xml name="sam_tag_validator">\n+\n+ <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>\n+ </xml>\n+ <xml name="sam_sort_order">\n+ <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">\n+ <option value="TemplateCoordinate">TemplateCoordinate</option>\n+ <option value="Coordinate">Coordinate</option>\n+ <option value="Queryname">Queryname</option>\n+ <option value="Random">Random</option>\n+ <option value="RandomQuery">RandomQuery</option>\n+ </param>\n+ </xml>\n+ \n+ <xml name="sort_order_change_format">\n+ <change_format>\n+ <when input="sort_order" value="Coordinate" format="bam" />\n+ <when input="sort_order" value="TemplateCoordinate" format="bam" />\n+ <when input="sort_order" value="QueryName" format="unsorted.bam" />\n+ <when input="sort_order" value="Random" format="unsorted.bam" />\n+ <when input="sort_order" value="RandomQuery" format="unsorted.bam" />\n+ </change_format>\n+ </xml>\n+\n+ <token name="@READ_STRUCTURES_HELP@"><![CDATA[\n+**Read Structures**\n+\n+Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:\n+\n+ - T identifies a template read\n+ - B identifies a sample barcode read\n+ - M identifies a unique molecular index read\n+ - S identifies a set of bases that should be skipped or ignored\n+\n+The last <number><operator> pair may be specified using a + sign instead of number to denote \xe2\x80\x9call remaining bases\xe2\x80\x9d. 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:\n+\n+:: \n+\n+ --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B\n+\n+Alternative if you know your reads are of fixed length you could specify:\n+\n+:: \n+\n+ --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B\n+\n+\n+]]></token>\n+ <xml name="citations">\n+ <citations>\n+ <yield />\n+ </citations>\n+ </xml>\n+</macros>\n' |