| Previous changeset 70:f383ca1c5033 (2019-11-05) Next changeset 72:8ef26717ba8b (2020-01-11) |
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Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 11ea16568d776a1dd68bb1ead50695ea8769f201" |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml normalize_readsizes.xml plot_coverage.xml update_mapq.xml write_supplementary_fastq.xml |
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| diff -r f383ca1c5033 -r b090e190c813 add_matesequence.xml --- a/add_matesequence.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/add_matesequence.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.17"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.18"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r f383ca1c5033 -r b090e190c813 allow_dovetailing.xml --- a/allow_dovetailing.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/allow_dovetailing.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.17"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.18"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r f383ca1c5033 -r b090e190c813 bam_readtagger.xml --- a/bam_readtagger.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/bam_readtagger.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.17"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.18"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r f383ca1c5033 -r b090e190c813 extract_variants.xml --- a/extract_variants.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/extract_variants.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="extract_variants" name="Extract variant fragments" version="0.5.17"> +<tool id="extract_variants" name="Extract variant fragments" version="0.5.18"> <description>from long reads</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r f383ca1c5033 -r b090e190c813 filter_insertions.xml --- a/filter_insertions.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/filter_insertions.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.17"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.18"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r f383ca1c5033 -r b090e190c813 findcluster.xml --- a/findcluster.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/findcluster.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.17"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.18"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r f383ca1c5033 -r b090e190c813 normalize_readsizes.xml --- a/normalize_readsizes.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/normalize_readsizes.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.17"> +<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.18"> <description>of multiple fastq files</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>normalize_readsizes --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r f383ca1c5033 -r b090e190c813 plot_coverage.xml --- a/plot_coverage.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/plot_coverage.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.17"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.18"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r f383ca1c5033 -r b090e190c813 update_mapq.xml --- a/update_mapq.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/update_mapq.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.5.17"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.18"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r f383ca1c5033 -r b090e190c813 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Tue Nov 05 05:06:18 2019 -0500 +++ b/write_supplementary_fastq.xml Wed Dec 18 09:27:51 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.17"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.18"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.5.17">readtagger</requirement> + <requirement type="package" version="0.5.18">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |