| Previous changeset 68:47e4891b11dd (2019-09-04) Next changeset 70:f383ca1c5033 (2019-11-05) |
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Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5071cc844a6999040ea605deb2eb88aafb7fb16b" |
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modified:
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 |
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| diff -r 47e4891b11dd -r 97411db5f752 add_matesequence.xml --- a/add_matesequence.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/add_matesequence.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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[ |
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| diff -r 47e4891b11dd -r 97411db5f752 allow_dovetailing.xml --- a/allow_dovetailing.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/allow_dovetailing.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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' |
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| diff -r 47e4891b11dd -r 97411db5f752 bam_readtagger.xml --- a/bam_readtagger.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/bam_readtagger.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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 |
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| diff -r 47e4891b11dd -r 97411db5f752 extract_variants.xml --- a/extract_variants.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/extract_variants.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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[ |
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| diff -r 47e4891b11dd -r 97411db5f752 filter_insertions.xml --- a/filter_insertions.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/filter_insertions.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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[ |
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| diff -r 47e4891b11dd -r 97411db5f752 findcluster.xml --- a/findcluster.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/findcluster.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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[ |
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| diff -r 47e4891b11dd -r 97411db5f752 plot_coverage.xml --- a/plot_coverage.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/plot_coverage.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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 |
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| diff -r 47e4891b11dd -r 97411db5f752 test-data/three_cluster_out.gff --- a/test-data/three_cluster_out.gff Wed Sep 04 06:17:51 2019 -0400 +++ b/test-data/three_cluster_out.gff Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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 |
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| diff -r 47e4891b11dd -r 97411db5f752 update_mapq.xml --- a/update_mapq.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/update_mapq.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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[ |
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| diff -r 47e4891b11dd -r 97411db5f752 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Wed Sep 04 06:17:51 2019 -0400 +++ b/write_supplementary_fastq.xml Thu Sep 05 10:22:27 2019 -0400 |
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| @@ -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[ |