Mercurial > repos > iuc > mummer_delta_filter

diff macros.xml @ 4:e8fdceffea4c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author iuc
date Mon, 18 Mar 2024 12:41:50 +0000
parents fbca557a4847
children
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line diff
--- a/macros.xml	Sat Nov 27 09:58:32 2021 +0000
+++ b/macros.xml	Mon Mar 18 12:41:50 2024 +0000
@@ -2,7 +2,7 @@
     <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
     <xml name="bio_tools">
         <xrefs>
-            <xref type="bio.tools">mumer4</xref>
+            <xref type="bio.tools">mummer4</xref>
         </xrefs>
     </xml>
     <xml name="citation">
@@ -10,15 +10,16 @@
             <citation type="doi">10.1371/journal.pcbi.1005944</citation>
         </citations>
     </xml>
+    <token name="@TOOL_VERSION@">4.0.0rc1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@PROFILE@">20.05</token>
     <xml name="gnuplot_requirement">
-        <requirement type="package" version="5.4.1">gnuplot</requirement>
+        <requirement type="package" version="5.4.8">gnuplot</requirement>
     </xml>
-    <token name="@TOOL_VERSION@">4.0.0rc1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
             <yield />
         </requirements>
     </xml>
@@ -30,13 +31,13 @@
             <option value="">Color</option>
             <option value="-color">No color (-color)</option>
         </param>
-        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
+        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default dotplot." >
             <option value="">Dotplot</option>
             <option value="-c">Coverage Plot (-c)</option>
         </param>
-        <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
+        <param type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
             help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
-        <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
+        <param type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
         <conditional name="labels" >
             <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
                 <option value="no">NO</option>
@@ -54,7 +55,7 @@
             <option value="large">Large</option>
         </param>
         <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
-        <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
+        <param type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
         <conditional name="range" >
             <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
                 <option value="no">NO</option>