| Previous changeset 20:03415763c62c (2017-04-19) Next changeset 22:42fefb316c95 (2017-04-23) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c9d087e79391f68feb0855ef87adc39ff54fbdab-dirty |
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modified:
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 |
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| diff -r 03415763c62c -r 1c91108a80d5 add_matesequence.xml --- a/add_matesequence.xml Wed Apr 19 16:23:12 2017 -0400 +++ b/add_matesequence.xml Thu Apr 20 11:04:08 2017 -0400 |
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| @@ -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[ |
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| diff -r 03415763c62c -r 1c91108a80d5 allow_dovetailing.xml --- a/allow_dovetailing.xml Wed Apr 19 16:23:12 2017 -0400 +++ b/allow_dovetailing.xml Thu Apr 20 11:04:08 2017 -0400 |
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| @@ -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' |
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| diff -r 03415763c62c -r 1c91108a80d5 bam_readtagger.xml --- a/bam_readtagger.xml Wed Apr 19 16:23:12 2017 -0400 +++ b/bam_readtagger.xml Thu Apr 20 11:04:08 2017 -0400 |
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| @@ -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 |
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| diff -r 03415763c62c -r 1c91108a80d5 findcluster.xml --- a/findcluster.xml Wed Apr 19 16:23:12 2017 -0400 +++ b/findcluster.xml Thu Apr 20 11:04:08 2017 -0400 |
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| @@ -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[ |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/a_pasteurianus_tagged_with_dm6.bam |
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| Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam |
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| Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/a_pasteurianus_tagged_with_dm6_verified.bam |
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| Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/dm6_mate_annotated.bam |
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| Binary file test-data/dm6_mate_annotated.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/dm6_tagged_with_a_pasteurianus.bam |
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| Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/dm6_tagged_with_a_pasteurianus_discarded.bam |
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| Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/dm6_tagged_with_a_pasteurianus_verified.bam |
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| Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/proper_pair.bam |
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| Binary file test-data/proper_pair.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/proper_pair_discard_out.bam |
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| Binary file test-data/proper_pair_discard_out.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/proper_pair_discard_verified_empty.bam |
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| Binary file test-data/proper_pair_discard_verified_empty.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/proper_pair_out_suboptimal_tags.bam |
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| Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/three_cluster_out.bam |
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| Binary file test-data/three_cluster_out.bam has changed |
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| diff -r 03415763c62c -r 1c91108a80d5 test-data/three_cluster_out.gff --- 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 |
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| @@ -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 |
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| diff -r 03415763c62c -r 1c91108a80d5 update_mapq.xml --- a/update_mapq.xml Wed Apr 19 16:23:12 2017 -0400 +++ b/update_mapq.xml Thu Apr 20 11:04:08 2017 -0400 |
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| @@ -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[ |
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| diff -r 03415763c62c -r 1c91108a80d5 write_supplementary_fastq.xml --- 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 |
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| @@ -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[ |