Mercurial > repos > jjohnson > fgbio_fastq_to_bam

annotate macros.xml @ 1:4635a93ebd91 draft

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"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
author jjohnson
date Wed, 24 Feb 2021 13:01:53 +0000
parents ee774248788f
children 6137ff37bea1
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
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11 <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
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12 <xml name="read_structures_validator">
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13 <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
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14 </xml>
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15 <xml name="sam_tag_validator">
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16 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
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17 </xml>
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18 <xml name="sam_sort_order">
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19 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
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20 <option value="TemplateCoordinate">TemplateCoordinate</option>
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21 <option value="Coordinate">Coordinate</option>
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22 <option value="Queryname">Queryname</option>
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23 <option value="Random">Random</option>
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24 <option value="RandomQuery">RandomQuery</option>
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25 </param>
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26 </xml>
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28 <xml name="sort_order_change_format">
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29 <change_format>
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30 <when input="sort_order" value="Coordinate" format="bam" />
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31 <when input="sort_order" value="TemplateCoordinate" format="bam" />
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32 <when input="sort_order" value="QueryName" format="unsorted.bam" />
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33 <when input="sort_order" value="Random" format="unsorted.bam" />
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34 <when input="sort_order" value="RandomQuery" format="unsorted.bam" />
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35 </change_format>
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36 </xml>
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38 <token name="@READ_STRUCTURES_HELP@"><![CDATA[
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39 **Read Structures**
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41 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
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42
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43 - T identifies a template read
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44 - B identifies a sample barcode read
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45 - M identifies a unique molecular index read
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46 - S identifies a set of bases that should be skipped or ignored
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48 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:
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50 ::
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52 --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
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54 Alternative if you know your reads are of fixed length you could specify:
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56 ::
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58 --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
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61 ]]></token>
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62 <xml name="citations">
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63 <citations>
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64 <yield />
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65 </citations>
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66 </xml>
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67 </macros>