Mercurial > repos > mvdbeek > bam_readtagger

changeset 64:31dc40ec7067 draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5071cc844a6999040ea605deb2eb88aafb7fb16b"
author mvdbeek
date Thu, 05 Sep 2019 10:21:59 -0400
parents 3cea8b694492
children 08a10eefc2ca
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml plot_coverage.xml test-data/three_cluster_out.gff update_mapq.xml write_supplementary_fastq.xml
diffstat 10 files changed, 22 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/add_matesequence.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.15">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.16">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/allow_dovetailing.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.15">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.16">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/bam_readtagger.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.15">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.16">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
--- a/extract_variants.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/extract_variants.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.15">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.16">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/filter_insertions.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/filter_insertions.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.15">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.16">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/findcluster.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/findcluster.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.15">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.16">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/plot_coverage.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.15">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.16">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
--- a/test-data/three_cluster_out.gff	Wed Sep 04 06:17:22 2019 -0400
+++ b/test-data/three_cluster_out.gff	Thu Sep 05 10:21:59 2019 -0400
@@ -1,8 +1,8 @@
 ##gff-version 3
-3R	findcluster	TE	13373206	13373206	2	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.010684606252473288,0.32977179791584227,0.6595435958316845;insert_reference_name=None;left_inserts=;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	findcluster	TE	13373206	13373206	2	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.010684606252473288,0.32977179791584227,0.6595435958316845;insert_reference_name=None;left_inserts=;left_mate_count=2;max_mapq=60;nref=0;proper_pair_only=False;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
 3R	find_softclip	3p_clip	13373515	13373514	7	+	.	ID=SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a;consensus=ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC;max_mapq=60
-3R	findcluster	TE	13373515	13373524	20	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=6.2761999508986e-30,1.9073449948406318e-06,0.9999980926550052;insert_reference_name=None;left_inserts=GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;right_inserts=GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;softclip_clusters=SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a,SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801;total_left_count=9;total_right_count=11;valid_TSD=False
+3R	findcluster	TE	13373515	13373524	20	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=6.2761999508986e-30,1.9073449948406318e-06,0.9999980926550052;insert_reference_name=None;left_inserts=GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;proper_pair_only=False;right_inserts=GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;softclip_clusters=SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a,SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801;total_left_count=9;total_right_count=11;valid_TSD=False
 3R	find_softclip	5p_clip	13373525	13373524	6	+	.	ID=SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801;consensus=CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT;max_mapq=60
-3R	findcluster	TE	13374539	13374676	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=homozygous;genotype_likelihoods=0.21259842519685054,0.3937007874015747;insert_reference_name=None;left_inserts=;left_mate_count=0;max_mapq=60;nref=0;right_inserts=;right_mate_count=1;softclip_clusters=;total_left_count=0;total_right_count=1;valid_TSD=False
-3R	findcluster	TE	13374595	13374709	2	+	.	ID=extended_and_annotated_roi.bam_3;genotype=homozygous;genotype_likelihoods=0.010684606252473288,0.32977179791584227,0.6595435958316845;insert_reference_name=None;left_inserts=GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	findcluster	TE	13374539	13374676	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=homozygous;genotype_likelihoods=0.21259842519685054,0.3937007874015747;insert_reference_name=None;left_inserts=;left_mate_count=0;max_mapq=60;nref=0;proper_pair_only=False;right_inserts=;right_mate_count=1;softclip_clusters=;total_left_count=0;total_right_count=1;valid_TSD=False
+3R	findcluster	TE	13374595	13374709	2	+	.	ID=extended_and_annotated_roi.bam_3;genotype=homozygous;genotype_likelihoods=0.010684606252473288,0.32977179791584227,0.6595435958316845;insert_reference_name=None;left_inserts=GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;proper_pair_only=False;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
 3R	find_softclip	5p_clip	13374677	13374676	1	+	.	ID=SOFTCLIP_extended_and_annotated_roi.bam_ad5ab08ae7f225f452b4e79bb9ab8425;consensus=TGGCAAAACATATGCAAAGTGCA;max_mapq=60
--- a/update_mapq.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/update_mapq.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.15">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.16">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml	Wed Sep 04 06:17:22 2019 -0400
+++ b/write_supplementary_fastq.xml	Thu Sep 05 10:21:59 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.15">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.16">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.15">readtagger</requirement>
+        <requirement type="package" version="0.5.16">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[