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

Changeset 60:01acf62d5012 (2019-08-29)
Previous changeset 59:13c5f2e30a13 (2019-08-28) Next changeset 61:210427d5c65a (2019-08-31)
Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit f8a3ec15a4b0f73bfab3510858bc21c264c0e79f"
modified:
add_matesequence.xml
allow_dovetailing.xml
bam_readtagger.xml
extract_variants.xml
filter_insertions.xml
findcluster.xml
plot_coverage.xml
update_mapq.xml
write_supplementary_fastq.xml
b
diff -r 13c5f2e30a13 -r 01acf62d5012 add_matesequence.xml
--- a/add_matesequence.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/add_matesequence.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.6">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.7">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 13c5f2e30a13 -r 01acf62d5012 allow_dovetailing.xml
--- a/allow_dovetailing.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/allow_dovetailing.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.6">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.7">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
b
diff -r 13c5f2e30a13 -r 01acf62d5012 bam_readtagger.xml
--- a/bam_readtagger.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/bam_readtagger.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.6">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.7">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
b
diff -r 13c5f2e30a13 -r 01acf62d5012 extract_variants.xml
--- a/extract_variants.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/extract_variants.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.6">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.7">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 13c5f2e30a13 -r 01acf62d5012 filter_insertions.xml
--- a/filter_insertions.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/filter_insertions.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.6">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.7">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 13c5f2e30a13 -r 01acf62d5012 findcluster.xml
--- a/findcluster.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/findcluster.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.6">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.7">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 13c5f2e30a13 -r 01acf62d5012 plot_coverage.xml
--- a/plot_coverage.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/plot_coverage.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.6">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.7">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
b
diff -r 13c5f2e30a13 -r 01acf62d5012 update_mapq.xml
--- a/update_mapq.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/update_mapq.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.6">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.7">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
b
diff -r 13c5f2e30a13 -r 01acf62d5012 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml Wed Aug 28 13:13:40 2019 -0400
+++ b/write_supplementary_fastq.xml Thu Aug 29 11:08:57 2019 -0400
[
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.6">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.7">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.6">readtagger</requirement>
+        <requirement type="package" version="0.5.7">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[