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changeset 18:a201937caf2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
author iuc
date Wed, 31 Jul 2019 14:19:38 -0400
parents 3263a2b5d9f0
children 54273c027875
files samtool_filter2.xml
diffstat 1 files changed, 19 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/samtool_filter2.xml	Wed Jun 06 18:43:15 2018 -0400
+++ b/samtool_filter2.xml	Wed Jul 31 14:19:38 2019 -0400
@@ -1,8 +1,24 @@
-<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8">
+<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8+galaxy1">
     <description>files on FLAG MAPQ RG LN or by region</description>
     <requirements>
         <requirement type="package" version="1.8">samtools</requirement>
     </requirements>
+    <macros>
+        <xml name="flag_options">
+            <option value="0x0001">Read is paired</option>
+            <option value="0x0002">Read is mapped in a proper pair</option>
+            <option value="0x0004">The read is unmapped</option>
+            <option value="0x0008">The mate is unmapped</option>
+            <option value="0x0010">Read is mapped to the reverse strand of the reference</option>
+            <option value="0x0020">Mate is mapped to the reverse strand of the reference</option>
+            <option value="0x0040">Read is the first in a pair</option>
+            <option value="0x0080">Read is the second in a pair</option>
+            <option value="0x0100">The alignment of this read is not primary</option>
+            <option value="0x0200">The read fails platform/vendor quality checks</option>
+            <option value="0x0400">The read is a PCR or optical duplicate</option>
+            <option value="0x0800">Supplementary alignment</option>
+        </xml>
+    </macros>
     <command detect_errors="exit_code"><![CDATA[
 ##set up input files, regions requires input.bam and input.bai
 #if $input1.is_of_type('bam')
@@ -78,32 +94,10 @@
             <when value="no"/>
             <when value="yes">
                 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)">
-                    <option value="0x0001">Read is paired</option>
-                    <option value="0x0002">Read is mapped in a proper pair</option>
-                    <option value="0x0004">The read is unmapped</option>
-                    <option value="0x0008">The mate is unmapped</option>
-                    <option value="0x0010">Read strand</option>
-                    <option value="0x0020">Mate strand</option>
-                    <option value="0x0040">Read is the first in a pair</option>
-                    <option value="0x0080">Read is the second in a pair</option>
-                    <option value="0x0100">The alignment or this read is not primary</option>
-                    <option value="0x0200">The read fails platform/vendor quality checks</option>
-                    <option value="0x0400">The read is a PCR or optical duplicate</option>
-                    <option value="0x0800">Supplementary alignment</option>
+                    <expand macro="flag_options" />
                 </param>
                 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)">
-                    <option value="0x0001">Read is paired</option>
-                    <option value="0x0002">Read is mapped in a proper pair</option>
-                    <option value="0x0004">The read is unmapped</option>
-                    <option value="0x0008">The mate is unmapped</option>
-                    <option value="0x0010">Read strand</option>
-                    <option value="0x0020">Mate strand</option>
-                    <option value="0x0040">Read is the first in a pair</option>
-                    <option value="0x0080">Read is the second in a pair</option>
-                    <option value="0x0100">The alignment or this read is not primary</option>
-                    <option value="0x0200">The read fails platform/vendor quality checks</option>
-                    <option value="0x0400">The read is a PCR or optical duplicate</option>
-                    <option value="0x0800">Supplementary alignment</option>
+                    <expand macro="flag_options" />
                 </param>
             </when>
         </conditional>