diff macros.xml.bak @ 2:f8798f04ac47 draft default tip

"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"

--- a/macros.xml.bak	Wed Feb 24 13:02:43 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>