Mercurial > repos > jjohnson > fgbio_sort_bam
diff fgbio_sort_bam.xml @ 0:286e35cf3f1c draft
"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
author | jjohnson |
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date | Sun, 21 Feb 2021 23:41:16 +0000 |
parents | |
children | cb58d1961fd3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fgbio_sort_bam.xml Sun Feb 21 23:41:16 2021 +0000 @@ -0,0 +1,34 @@ +<tool id="fgbio_sort_bam" name="fgbio SortBam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description>Sorts a SAM or BAM file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>fgbio --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + fgbio SortBam" + --input '$input' + --sort-order=$sort_order + --output '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="bam,sam" label="SAM/BAM to sort"/> + <expand macro="sam_sort_order" /> + </inputs> + <outputs> + <data name="output" format="unsorted.bam" /> + </outputs> + <help><![CDATA[ +**fgbio SortBam** + +Sorts a SAM or BAM file. Several sort orders are available: + + - Coordinate: sorts reads by their reference sequence and left-most aligned coordinate + - Queryname: sort the reads by their query (i.e. read) name + - Random: sorts the reads into a random order. The output is deterministic for any given input. and several + - RandomQuery: sorts the reads into a random order but keeps reads with the same queryname together. The ordering is deterministic for any given input. + +http://fulcrumgenomics.github.io/fgbio/tools/latest/SortBam.html + ]]></help> + <expand macro="citations" /> +</tool>