Mercurial > repos > mvdbeek > bam_readtagger

changeset 56:b50e114fece9 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c3a7b2f6aa429ea2881ee8d111ace3cce95bb9e7
author mvdbeek
date Sun, 28 Jul 2019 15:59:14 -0400
parents 5c96f12f837d
children 38ae00c376ef
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml plot_coverage.xml test-data/extended_and_annotated_roi.bam.bai test-data/out.png test-data/three_cluster_out.bam.bai update_mapq.xml write_supplementary_fastq.xml
diffstat 12 files changed, 18 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/add_matesequence.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.2">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.3">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/allow_dovetailing.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.2">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.3">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/bam_readtagger.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.2">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.3">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
--- a/extract_variants.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/extract_variants.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.2">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.3">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/filter_insertions.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/filter_insertions.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.2">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.3">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/findcluster.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/findcluster.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.2">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.3">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/plot_coverage.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.2">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.3">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
Binary file test-data/out.png has changed
Binary file test-data/three_cluster_out.bam.bai has changed
--- a/update_mapq.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/update_mapq.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.2">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.3">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/write_supplementary_fastq.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.2">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.3">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[