Mercurial > repos > devteam > bamtools_filter

changeset 9:1dfd95ee241e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
author iuc
date Sat, 27 Nov 2021 10:02:24 +0000
parents cb20f99fd45b
children 108db6635177
files bamtools-filter.xml macros.xml
diffstat 2 files changed, 27 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/bamtools-filter.xml	Thu Feb 20 17:23:24 2020 -0500
+++ b/bamtools-filter.xml	Sat Nov 27 10:02:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="bamFilter" name="Filter" version="2.4.1">
+<tool id="bamFilter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>BAM datasets on a variety of attributes</description>
     <macros>
           <import>macros.xml</import>
@@ -41,28 +41,28 @@
             <repeat name="filters" title="Filter" min="1">
                 <conditional name="bam_property">
                     <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
-                        <option value="alignmentFlag"/>
-                        <option value="cigar"/>
-                        <option value="insertSize"/>
-                        <option value="isDuplicate"/>
-                        <option value="isFailedQC"/>
-                        <option value="isFirstMate"/>
-                        <option value="isMapped"/>
-                        <option value="isMateMapped"/>
-                        <option value="isMateReverseStrand"/>
-                        <option value="isPaired"/>
-                        <option value="isPrimaryAlignment"/>
-                        <option value="isProperPair"/>
-                        <option value="isReverseStrand"/>
-                        <option value="isSecondMate"/>
-                        <option selected="True" value="mapQuality"/>
-                        <option value="matePosition"/>
-                        <option value="mateReference"/>
-                        <option value="name"/>
-                        <option value="position"/>
-                        <option value="queryBases"/>
-                        <option value="reference"/>
-                        <option value="tag"/>
+                        <option value="alignmentFlag">Alignment flag</option>
+                        <option value="cigar">CIGAR string</option>
+                        <option value="insertSize">Insert size</option>
+                        <option value="isDuplicate">Duplicate</option>
+                        <option value="isFailedQC">Quality check</option>
+                        <option value="isFirstMate">First mate</option>
+                        <option value="isMapped">Mapped</option>
+                        <option value="isMateMapped">Mate mapped</option>
+                        <option value="isMateReverseStrand">Mate is on reverse strand</option>
+                        <option value="isPaired">Paired</option>
+                        <option value="isPrimaryAlignment">Primary alignment</option>
+                        <option value="isProperPair">Proper pair</option>
+                        <option value="isReverseStrand">Reverse strand</option>
+                        <option value="isSecondMate">Second mate</option>
+                        <option selected="true" value="mapQuality">Mapping quality</option>
+                        <option value="matePosition">Position of the mate</option>
+                        <option value="mateReference">Reference name of the mate</option>
+                        <option value="name">Read name</option>
+                        <option value="position">Position of the read</option>
+                        <option value="queryBases">Sequence motif</option>
+                        <option value="reference">Reference name of the read</option>
+                        <option value="tag">Tag</option>
                     </param>
                     <!-- would be fanstastic to have AND and OR constructs in when statements -->
                     <when value="alignmentFlag">
@@ -79,7 +79,7 @@
                         </param>
                     </when>
                     <when value="isDuplicate">
-                        <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />
+                        <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads marked as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />
                     </when>
                     <when value="isFailedQC">
                         <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>
--- a/macros.xml	Thu Feb 20 17:23:24 2020 -0500
+++ b/macros.xml	Sat Nov 27 10:02:24 2021 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">2.4.0</token>
+    <token name="@TOOL_VERSION@">2.5.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">bamtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bamtools</requirement>
             <requirement type="package" version="1.4.1">samtools</requirement>
         </requirements>
     </xml>