changeset 5:5831b4b77d08 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_fixmate commit 17b880b5009a80a117eb6534bb95cd5795ed0321

--- a/macros.xml	Sun Sep 08 03:22:41 2024 +0000
+++ b/macros.xml	Thu Feb 19 20:24:42 2026 +0000
@@ -11,9 +11,9 @@
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
-    <token name="@TOOL_VERSION@">1.20</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">22.05</token>
+    <token name="@TOOL_VERSION@">1.22</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">24.0</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
@@ -167,6 +167,18 @@
     <xml name="seed_input">
        <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
     </xml>
+
+    <!-- Include/exclude by flags + flag options -->
+    <xml name="inclusive_filter_macro" token_argument="">
+        <param name="inclusive_filter" argument="@ARGUMENT@" type="select" multiple="True" label="Require that these flags are set">
+            <expand macro="flag_options" />
+        </param>
+    </xml>
+    <xml name="exclusive_filter_macro" token_argument="">
+        <param name="exclusive_filter" argument="@ARGUMENT@" type="select" multiple="True" label="Exclude reads with any of the following flags set">
+            <expand macro="flag_options" />
+        </param>
+    </xml>
     <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
         <option value="1" selected="@S1@">Read is paired</option>
         <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
@@ -220,6 +232,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/gigascience/giab008</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
         </citations>
     </xml>
     <xml name="version_command">

--- 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 -");-->