Mercurial > repos > jjohnson > fgbio_sort_bam

diff fgbio_sort_bam.xml @ 1:cb58d1961fd3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
author jjohnson
date Wed, 24 Feb 2021 13:02:43 +0000
parents 286e35cf3f1c
children
line wrap: on
line diff
--- a/fgbio_sort_bam.xml	Sun Feb 21 23:41:16 2021 +0000
+++ b/fgbio_sort_bam.xml	Wed Feb 24 13:02:43 2021 +0000
@@ -6,17 +6,23 @@
     <expand macro="requirements" />
     <version_command>fgbio --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        fgbio SortBam" 
+        fgbio SortBam 
         --input '$input'
-        --sort-order=$sort_order
+        #if $sort_order
+            --sort-order=$sort_order
+        #end if
         --output '$output'
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="bam,sam" label="SAM/BAM to sort"/>
+        <param name="input" type="data" format="unsorted.bam,bam,sam" label="SAM/BAM to sort"/>
         <expand macro="sam_sort_order" />
     </inputs>
     <outputs>
-        <data name="output" format="unsorted.bam" />
+        <data name="output" format="unsorted.bam" >
+            <!--
+            <expand macro="sort_order_change_format" />
+            -->
+        </data>
     </outputs>
     <help><![CDATA[
 **fgbio SortBam**