| Previous changeset 46:4ebfef7b3488 (2019-01-15) Next changeset 48:72c9afb724a6 (2019-02-10) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit ff53a7c7582a4dfda1bfcc0c8832b4edc223bc5e |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml filter_insertions.xml findcluster.xml plot_coverage.xml update_mapq.xml write_supplementary_fastq.xml |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d add_matesequence.xml --- a/add_matesequence.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/add_matesequence.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.15"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.16"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d allow_dovetailing.xml --- a/allow_dovetailing.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/allow_dovetailing.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.15"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.16"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d bam_readtagger.xml --- a/bam_readtagger.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/bam_readtagger.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.15"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.16"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s @@ -23,9 +23,9 @@ -o '$tagged_file' ]]></command> <inputs> - <param name="tag_file" argument="--tag_file" type="data" format="bam"/> + <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_input_sorted.bam"/> <repeat name="alignment_series" title="Alignments"> - <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/> + <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_input_sorted.bam"/> <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> <expand macro="tag_options"/> </param> |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d filter_insertions.xml --- a/filter_insertions.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/filter_insertions.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.15"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.16"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d findcluster.xml --- a/findcluster.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/findcluster.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.15"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.16"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d plot_coverage.xml --- a/plot_coverage.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/plot_coverage.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.4.15"> +<tool id="plot_coverage" name="Plot coverage" version="0.4.16"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d update_mapq.xml --- a/update_mapq.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/update_mapq.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.15"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.16"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 4ebfef7b3488 -r a4e30210fc3d write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Tue Jan 15 14:03:29 2019 -0500 +++ b/write_supplementary_fastq.xml Mon Jan 28 03:26:58 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.15"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.16"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.15">readtagger</requirement> + <requirement type="package" version="0.4.16">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |