Mercurial > repos > mvdbeek > bam_readtagger

changeset 72:8ef26717ba8b draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 76af27eb69faaeffe6a9f20a40e112b42b5aed53"
author mvdbeek
date Sat, 11 Jan 2020 11:58:25 -0500
parents b090e190c813
children 676b7ff2d899
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml normalize_readsizes.xml plot_coverage.xml update_mapq.xml write_supplementary_fastq.xml
diffstat 10 files changed, 20 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/add_matesequence.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.18">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.19">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/allow_dovetailing.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.18">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.19">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/bam_readtagger.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.18">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.19">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
--- a/extract_variants.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/extract_variants.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.18">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.19">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/filter_insertions.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/filter_insertions.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.18">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.19">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/findcluster.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/findcluster.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.18">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.19">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/normalize_readsizes.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/normalize_readsizes.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.18">
+<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.19">
     <description>of multiple fastq files</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>normalize_readsizes --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/plot_coverage.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.18">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.19">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
--- a/update_mapq.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/update_mapq.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.18">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.19">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml	Wed Dec 18 09:27:51 2019 -0500
+++ b/write_supplementary_fastq.xml	Sat Jan 11 11:58:25 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.18">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.19">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.18">readtagger</requirement>
+        <requirement type="package" version="0.5.19">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[