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