Mercurial > repos > jjohnson > fgbio_sort_bam

annotate fgbio_sort_bam.xml @ 0:286e35cf3f1c draft

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"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
author jjohnson
date Sun, 21 Feb 2021 23:41:16 +0000
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children cb58d1961fd3
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286e35cf3f1c "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
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1 <tool id="fgbio_sort_bam" name="fgbio SortBam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>Sorts a SAM or BAM file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>fgbio --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 fgbio SortBam"
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10 --input '$input'
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11 --sort-order=$sort_order
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12 --output '$output'
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="bam,sam" label="SAM/BAM to sort"/>
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16 <expand macro="sam_sort_order" />
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="unsorted.bam" />
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20 </outputs>
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21 <help><![CDATA[
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22 **fgbio SortBam**
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23
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24 Sorts a SAM or BAM file. Several sort orders are available:
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25
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26 - Coordinate: sorts reads by their reference sequence and left-most aligned coordinate
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27 - Queryname: sort the reads by their query (i.e. read) name
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28 - Random: sorts the reads into a random order. The output is deterministic for any given input. and several
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29 - RandomQuery: sorts the reads into a random order but keeps reads with the same queryname together. The ordering is deterministic for any given input.
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30
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31 http://fulcrumgenomics.github.io/fgbio/tools/latest/SortBam.html
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32 ]]></help>
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33 <expand macro="citations" />
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34 </tool>