Repository 'bam_readtagger'
hg clone https://toolshed.g2.bx.psu.edu/repos/mvdbeek/bam_readtagger

Changeset 45:d475729e90ea (2019-01-15)
Previous changeset 44:4870f1d6f037 (2019-01-14) Next changeset 46:4ebfef7b3488 (2019-01-15)
Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 53ffd541eefb788d54435b15ae04210dde028dd5
modified:
add_matesequence.xml
allow_dovetailing.xml
bam_readtagger.xml
filter_insertions.xml
findcluster.xml
plot_coverage.xml
update_mapq.xml
write_supplementary_fastq.xml
added:
test-data/extended_and_annotated_roi.bam.bai
test-data/out.png
test-data/three_cluster_out.bam.bai
b
diff -r 4870f1d6f037 -r d475729e90ea add_matesequence.xml
--- a/add_matesequence.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/add_matesequence.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.13">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.14">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 4870f1d6f037 -r d475729e90ea allow_dovetailing.xml
--- a/allow_dovetailing.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/allow_dovetailing.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.13">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.14">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
b
diff -r 4870f1d6f037 -r d475729e90ea bam_readtagger.xml
--- a/bam_readtagger.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/bam_readtagger.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.13">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.14">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
b
diff -r 4870f1d6f037 -r d475729e90ea filter_insertions.xml
--- a/filter_insertions.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/filter_insertions.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.13">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.14">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 4870f1d6f037 -r d475729e90ea findcluster.xml
--- a/findcluster.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/findcluster.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.13">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.14">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 4870f1d6f037 -r d475729e90ea plot_coverage.xml
--- a/plot_coverage.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/plot_coverage.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.13">
+<tool id="plot_coverage" name="Plot coverage" version="0.4.14">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
b
diff -r 4870f1d6f037 -r d475729e90ea test-data/extended_and_annotated_roi.bam.bai
b
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
b
diff -r 4870f1d6f037 -r d475729e90ea test-data/out.png
b
Binary file test-data/out.png has changed
b
diff -r 4870f1d6f037 -r d475729e90ea test-data/three_cluster_out.bam.bai
b
Binary file test-data/three_cluster_out.bam.bai has changed
b
diff -r 4870f1d6f037 -r d475729e90ea update_mapq.xml
--- a/update_mapq.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/update_mapq.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.13">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.14">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 4870f1d6f037 -r d475729e90ea write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml Mon Jan 14 13:18:25 2019 -0500
+++ b/write_supplementary_fastq.xml Tue Jan 15 12:51:31 2019 -0500
[
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.13">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.14">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.13">readtagger</requirement>
+        <requirement type="package" version="0.4.14">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[