Mercurial > repos > jjohnson > fgbio_sort_bam
comparison fgbio_sort_bam.xml @ 1:cb58d1961fd3 draft
"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
| author | jjohnson |
|---|---|
| date | Wed, 24 Feb 2021 13:02:43 +0000 |
| parents | 286e35cf3f1c |
| children |
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| 0:286e35cf3f1c | 1:cb58d1961fd3 |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <version_command>fgbio --version</version_command> | 7 <version_command>fgbio --version</version_command> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 fgbio SortBam" | 9 fgbio SortBam |
| 10 --input '$input' | 10 --input '$input' |
| 11 --sort-order=$sort_order | 11 #if $sort_order |
| 12 --sort-order=$sort_order | |
| 13 #end if | |
| 12 --output '$output' | 14 --output '$output' |
| 13 ]]></command> | 15 ]]></command> |
| 14 <inputs> | 16 <inputs> |
| 15 <param name="input" type="data" format="bam,sam" label="SAM/BAM to sort"/> | 17 <param name="input" type="data" format="unsorted.bam,bam,sam" label="SAM/BAM to sort"/> |
| 16 <expand macro="sam_sort_order" /> | 18 <expand macro="sam_sort_order" /> |
| 17 </inputs> | 19 </inputs> |
| 18 <outputs> | 20 <outputs> |
| 19 <data name="output" format="unsorted.bam" /> | 21 <data name="output" format="unsorted.bam" > |
| 22 <!-- | |
| 23 <expand macro="sort_order_change_format" /> | |
| 24 --> | |
| 25 </data> | |
| 20 </outputs> | 26 </outputs> |
| 21 <help><![CDATA[ | 27 <help><![CDATA[ |
| 22 **fgbio SortBam** | 28 **fgbio SortBam** |
| 23 | 29 |
| 24 Sorts a SAM or BAM file. Several sort orders are available: | 30 Sorts a SAM or BAM file. Several sort orders are available: |