| Previous changeset 21:1c91108a80d5 (2017-04-20) Next changeset 23:1323ffbc8785 (2017-04-25) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 16f35b0e373f4cbd33f1bc6aef4a13b7fd2eca12-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_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_discard_out.bam test-data/proper_pair_discard_verified_empty.bam test-data/proper_pair_out_suboptimal_tags.bam update_mapq.xml write_supplementary_fastq.xml |
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| diff -r 1c91108a80d5 -r 42fefb316c95 add_matesequence.xml --- a/add_matesequence.xml Thu Apr 20 11:04:08 2017 -0400 +++ b/add_matesequence.xml Sun Apr 23 15:58:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.15"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.16"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.15">readtagger</requirement> + <requirement type="package" version="0.3.16">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 1c91108a80d5 -r 42fefb316c95 allow_dovetailing.xml --- a/allow_dovetailing.xml Thu Apr 20 11:04:08 2017 -0400 +++ b/allow_dovetailing.xml Sun Apr 23 15:58:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.15"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.16"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.15">readtagger</requirement> + <requirement type="package" version="0.3.16">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 1c91108a80d5 -r 42fefb316c95 bam_readtagger.xml --- a/bam_readtagger.xml Thu Apr 20 11:04:08 2017 -0400 +++ b/bam_readtagger.xml Sun Apr 23 15:58:53 2017 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.15"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.16"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.15">readtagger</requirement> + <requirement type="package" version="0.3.16">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a @@ -16,6 +16,7 @@ $discarded $verified $discard_proper_pairs + --cores "\${GALAXY_SLOTS:-2}" -o '$tagged_file' ]]></command> <inputs> |
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| diff -r 1c91108a80d5 -r 42fefb316c95 findcluster.xml --- a/findcluster.xml Thu Apr 20 11:04:08 2017 -0400 +++ b/findcluster.xml Sun Apr 23 15:58:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.15"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.16"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.15">readtagger</requirement> + <requirement type="package" version="0.3.16">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 1c91108a80d5 -r 42fefb316c95 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 1c91108a80d5 -r 42fefb316c95 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam |
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| diff -r 1c91108a80d5 -r 42fefb316c95 test-data/a_pasteurianus_tagged_with_dm6_verified.bam |
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| diff -r 1c91108a80d5 -r 42fefb316c95 test-data/dm6_tagged_with_a_pasteurianus.bam |
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| diff -r 1c91108a80d5 -r 42fefb316c95 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 1c91108a80d5 -r 42fefb316c95 test-data/dm6_tagged_with_a_pasteurianus_verified.bam |
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| diff -r 1c91108a80d5 -r 42fefb316c95 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 1c91108a80d5 -r 42fefb316c95 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 1c91108a80d5 -r 42fefb316c95 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 1c91108a80d5 -r 42fefb316c95 update_mapq.xml --- a/update_mapq.xml Thu Apr 20 11:04:08 2017 -0400 +++ b/update_mapq.xml Sun Apr 23 15:58:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.15"> +<tool id="update_mapq" name="Update MAPQ score" version="0.3.16"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.15">readtagger</requirement> + <requirement type="package" version="0.3.16">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 1c91108a80d5 -r 42fefb316c95 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Thu Apr 20 11:04:08 2017 -0400 +++ b/write_supplementary_fastq.xml Sun Apr 23 15:58:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.15"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.16"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.15">readtagger</requirement> + <requirement type="package" version="0.3.16">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |