| Previous changeset 18:8fef53971086 (2017-04-03) Next changeset 20:03415763c62c (2017-04-19) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh findcluster.xml update_mapq.xml write_supplementary_fastq.xml |
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| diff -r 8fef53971086 -r 97c1b92dbd28 add_matesequence.xml --- a/add_matesequence.xml Mon Apr 03 09:42:31 2017 -0400 +++ b/add_matesequence.xml Wed Apr 05 17:34:55 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.12"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.13"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.12">readtagger</requirement> + <requirement type="package" version="0.3.13">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 8fef53971086 -r 97c1b92dbd28 allow_dovetailing.xml --- a/allow_dovetailing.xml Mon Apr 03 09:42:31 2017 -0400 +++ b/allow_dovetailing.xml Wed Apr 05 17:34:55 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.12"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.13"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.12">readtagger</requirement> + <requirement type="package" version="0.3.13">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 8fef53971086 -r 97c1b92dbd28 bam_readtagger.xml --- a/bam_readtagger.xml Mon Apr 03 09:42:31 2017 -0400 +++ b/bam_readtagger.xml Wed Apr 05 17:34:55 2017 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.12"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.13"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.12">readtagger</requirement> + <requirement type="package" version="0.3.13">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a |
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| diff -r 8fef53971086 -r 97c1b92dbd28 findcluster.xml --- a/findcluster.xml Mon Apr 03 09:42:31 2017 -0400 +++ b/findcluster.xml Wed Apr 05 17:34:55 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.12"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.13"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.12">readtagger</requirement> + <requirement type="package" version="0.3.13">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -14,6 +14,7 @@ #end if --output_bam '$output_bam' --output_gff '$output_gff' + --output_fasta '$output_fasta' --sample_name '$input.element_identifier' --threads "\${GALAXY_SLOTS:-2}" ]]></command> @@ -23,6 +24,7 @@ </inputs> <outputs> <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> + <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/> <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> </outputs> <tests> |
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| diff -r 8fef53971086 -r 97c1b92dbd28 update_mapq.xml --- a/update_mapq.xml Mon Apr 03 09:42:31 2017 -0400 +++ b/update_mapq.xml Wed Apr 05 17:34:55 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.12"> +<tool id="update_mapq" name="Update MAPQ score" version="0.3.13"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.12">readtagger</requirement> + <requirement type="package" version="0.3.13">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 8fef53971086 -r 97c1b92dbd28 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Mon Apr 03 09:42:31 2017 -0400 +++ b/write_supplementary_fastq.xml Wed Apr 05 17:34:55 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.12"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.13"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.12">readtagger</requirement> + <requirement type="package" version="0.3.13">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |