# HG changeset patch
# User mvdbeek
# Date 1492633392 14400
# Node ID 03415763c62cca3d26fb6af8ea0c1c03be89f86a
# Parent  97c1b92dbd2843cc4f637a567f4939044b1b2403
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty

diff -r 97c1b92dbd28 -r 03415763c62c add_matesequence.xml
--- a/add_matesequence.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/add_matesequence.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.13">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.14">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 97c1b92dbd28 -r 03415763c62c allow_dovetailing.xml
--- a/allow_dovetailing.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/allow_dovetailing.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.13">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.14">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
@@ -15,7 +15,7 @@
     <tests>
         <test>
             <param name="input" value="not_a_proper_pair.bam" ftype="bam"/>
-            <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 97c1b92dbd28 -r 03415763c62c bam_readtagger.xml
--- a/bam_readtagger.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/bam_readtagger.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.13">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.14">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
@@ -54,9 +54,9 @@
             </repeat>
             <param name="discarded" value="True"/>
             <param name="verified" value="True"/>
-            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/>
-            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/>
-            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/>
+            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/>
+            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/>
+            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/>
         </test>
         <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) -->
             <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
@@ -67,9 +67,9 @@
             </repeat>
             <param name="discarded" value="True"/>
             <param name="verified" value="True"/>
-            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" />
-            <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/>
-            <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
+            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" />
+            <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/>
+            <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/>
         </test>
         <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
             <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
@@ -82,9 +82,9 @@
             <param name="keep_suboptimal" value="True"/>
             <param name="discard_proper_pairs" value="True"/>
             <param name="verified" value="True"/>
-            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" />
-            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/>
-            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/>
+            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" />
+            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/>
+            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 97c1b92dbd28 -r 03415763c62c findcluster.xml
--- a/findcluster.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/findcluster.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.13">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.14">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 97c1b92dbd28 -r 03415763c62c update_mapq.xml
--- a/update_mapq.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/update_mapq.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.13">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.14">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 97c1b92dbd28 -r 03415763c62c write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/write_supplementary_fastq.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.13">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.14">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[