Mercurial > repos > iuc > samtools_fixmate

diff samtools_fixmate.xml @ 5:5831b4b77d08 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_fixmate commit 17b880b5009a80a117eb6534bb95cd5795ed0321
author iuc
date Thu, 19 Feb 2026 20:24:42 +0000
parents bb39588ae743
children
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--- a/samtools_fixmate.xml	Sun Sep 08 03:22:41 2024 +0000
+++ b/samtools_fixmate.xml	Thu Feb 19 20:24:42 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>fill mate coordinates, ISIZE and mate related flags</description>
     <macros>
         <import>macros.xml</import>
@@ -31,7 +31,7 @@
             '$output'
     ]]></command>
     <inputs>
-        <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
+        <param name="bamfile" type="data" format="sam,unsorted.bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
         <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" />
         <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
         <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
@@ -61,13 +61,13 @@
         <!--    test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
         <test>
             <param name="bamfile" value="5_ct.sam" ftype="sam" />
-            <param name="tempcigar" value="-c" />
+            <param name="tempcigar" value="true" />
             <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
         </test>
         <!--    test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
         <test>
             <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
-            <param name="tempcigar" value="-c" />
+            <param name="tempcigar" value="true" />
             <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
         </test>
         <!--    test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->