Mercurial > repos > mvdbeek > bam_readtagger

changeset 21:1c91108a80d5 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c9d087e79391f68feb0855ef87adc39ff54fbdab-dirty
author mvdbeek
date Thu, 20 Apr 2017 11:04:08 -0400
parents 03415763c62c
children 42fefb316c95
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml test-data/a_pasteurianus_tagged_with_dm6.bam test-data/a_pasteurianus_tagged_with_dm6_discarded.bam test-data/a_pasteurianus_tagged_with_dm6_verified.bam test-data/dm6_mate_annotated.bam test-data/dm6_tagged_with_a_pasteurianus.bam test-data/dm6_tagged_with_a_pasteurianus_discarded.bam test-data/dm6_tagged_with_a_pasteurianus_verified.bam test-data/proper_pair.bam test-data/proper_pair_discard_out.bam test-data/proper_pair_discard_verified_empty.bam test-data/proper_pair_out_suboptimal_tags.bam test-data/three_cluster_out.bam test-data/three_cluster_out.gff update_mapq.xml write_supplementary_fastq.xml
diffstat 19 files changed, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Wed Apr 19 16:23:12 2017 -0400
+++ b/add_matesequence.xml	Thu Apr 20 11:04:08 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.14">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.15">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.14">readtagger</requirement>
+        <requirement type="package" version="0.3.15">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Wed Apr 19 16:23:12 2017 -0400
+++ b/allow_dovetailing.xml	Thu Apr 20 11:04:08 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.14">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.15">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.14">readtagger</requirement>
+        <requirement type="package" version="0.3.15">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Wed Apr 19 16:23:12 2017 -0400
+++ b/bam_readtagger.xml	Thu Apr 20 11:04:08 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.14">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.15">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.14">readtagger</requirement>
+        <requirement type="package" version="0.3.15">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
--- a/findcluster.xml	Wed Apr 19 16:23:12 2017 -0400
+++ b/findcluster.xml	Thu Apr 20 11:04:08 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.14">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.15">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.14">readtagger</requirement>
+        <requirement type="package" version="0.3.15">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed
Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed
Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed
Binary file test-data/dm6_mate_annotated.bam has changed
Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed
Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed
Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed
Binary file test-data/proper_pair.bam has changed
Binary file test-data/proper_pair_discard_out.bam has changed
Binary file test-data/proper_pair_discard_verified_empty.bam has changed
Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed
Binary file test-data/three_cluster_out.bam has changed
--- a/test-data/three_cluster_out.gff	Wed Apr 19 16:23:12 2017 -0400
+++ b/test-data/three_cluster_out.gff	Thu Apr 20 11:04:08 2017 -0400
@@ -1,4 +1,4 @@
 ##gff-version 3
-3R	findcluster	TE	13373515	13373524	27	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=1.8828617809e-31,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=14;non_support=0;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False
+3R	findcluster	TE	13373515	13373524	22	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=1.8828617809e-31,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=11;non_support=0;right_insert=0,GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=11;valid_TSD=False
 3R	findcluster	TE	13374595	13374595	2	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=0.0106846062525,0.329771797916,0.659543595832;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;non_support=0;right_insert=;right_support=0;valid_TSD=False
 3R	findcluster	TE	13374677	13374677	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=heterozygous;genotype_likelihoods=0.212598425197,0.393700787402;left_insert=;left_support=0;non_support=0;right_insert=;right_support=1;valid_TSD=False
--- a/update_mapq.xml	Wed Apr 19 16:23:12 2017 -0400
+++ b/update_mapq.xml	Thu Apr 20 11:04:08 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.14">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.15">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.14">readtagger</requirement>
+        <requirement type="package" version="0.3.15">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml	Wed Apr 19 16:23:12 2017 -0400
+++ b/write_supplementary_fastq.xml	Thu Apr 20 11:04:08 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.14">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.15">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.14">readtagger</requirement>
+        <requirement type="package" version="0.3.15">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[