| Previous changeset 56:b50e114fece9 (2019-07-28) Next changeset 58:84f51c5d69e3 (2019-08-27) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8186814619b9163944e3c11cb797f02c94804ecb |
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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 update_mapq.xml write_supplementary_fastq.xml |
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| diff -r b50e114fece9 -r 38ae00c376ef add_matesequence.xml --- a/add_matesequence.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/add_matesequence.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.3"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.4"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b50e114fece9 -r 38ae00c376ef allow_dovetailing.xml --- a/allow_dovetailing.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/allow_dovetailing.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.3"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.4"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r b50e114fece9 -r 38ae00c376ef bam_readtagger.xml --- a/bam_readtagger.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/bam_readtagger.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.3"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.4"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r b50e114fece9 -r 38ae00c376ef extract_variants.xml --- a/extract_variants.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/extract_variants.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="extract_variants" name="Extract variant fragments" version="0.5.3"> +<tool id="extract_variants" name="Extract variant fragments" version="0.5.4"> <description>from long reads</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b50e114fece9 -r 38ae00c376ef filter_insertions.xml --- a/filter_insertions.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/filter_insertions.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.3"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.4"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b50e114fece9 -r 38ae00c376ef findcluster.xml --- a/findcluster.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/findcluster.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.3"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.4"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b50e114fece9 -r 38ae00c376ef plot_coverage.xml --- a/plot_coverage.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/plot_coverage.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.3"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.4"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r b50e114fece9 -r 38ae00c376ef update_mapq.xml --- a/update_mapq.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/update_mapq.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.5.3"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.4"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b50e114fece9 -r 38ae00c376ef write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Sun Jul 28 15:59:14 2019 -0400 +++ b/write_supplementary_fastq.xml Mon Jul 29 10:52:49 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.3"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.4"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.5.3">readtagger</requirement> + <requirement type="package" version="0.5.4">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |