| Previous changeset 42:5b8781514bc1 (2018-05-24) Next changeset 44:4870f1d6f037 (2019-01-14) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 7ee4c1dd4e13a4d634b0e80efdd2309289a29a1c |
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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 5b8781514bc1 -r 6f9b1b81b593 add_matesequence.xml --- a/add_matesequence.xml Thu May 24 11:51:27 2018 -0400 +++ b/add_matesequence.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.11"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.12"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5b8781514bc1 -r 6f9b1b81b593 allow_dovetailing.xml --- a/allow_dovetailing.xml Thu May 24 11:51:27 2018 -0400 +++ b/allow_dovetailing.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.11"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.12"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 5b8781514bc1 -r 6f9b1b81b593 bam_readtagger.xml --- a/bam_readtagger.xml Thu May 24 11:51:27 2018 -0400 +++ b/bam_readtagger.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,31 +1,31 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.11"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - readtagger -t '$tag_file' -s - #for $element in $alignment_series - '$element.annotate_with':$element.r_tag:$element.m_tag - #end for - #if $reference_fasta: - --reference_fasta '$reference_fasta' - #end if - $allow_dovetailing - $discard_suboptimal - $discarded - $verified - $discard_proper_pairs - --cores "\${GALAXY_SLOTS:-2}" - -o '$tagged_file' +readtagger -t '$tag_file' -s +#for $element in $alignment_series + '$element.annotate_with':$element.r_tag:$element.m_tag +#end for +#if $reference_fasta: + --reference_fasta '$reference_fasta' +#end if +$allow_dovetailing +$discard_suboptimal +$discarded +$verified +$discard_proper_pairs +--cores "\${GALAXY_SLOTS:-2}" +-o '$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="qname_sorted.bam,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="qname_sorted.bam,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 5b8781514bc1 -r 6f9b1b81b593 filter_insertions.xml --- a/filter_insertions.xml Thu May 24 11:51:27 2018 -0400 +++ b/filter_insertions.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.11"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.12"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5b8781514bc1 -r 6f9b1b81b593 findcluster.xml --- a/findcluster.xml Thu May 24 11:51:27 2018 -0400 +++ b/findcluster.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.11"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.12"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5b8781514bc1 -r 6f9b1b81b593 plot_coverage.xml --- a/plot_coverage.xml Thu May 24 11:51:27 2018 -0400 +++ b/plot_coverage.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.4.11"> +<tool id="plot_coverage" name="Plot coverage" version="0.4.12"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r 5b8781514bc1 -r 6f9b1b81b593 update_mapq.xml --- a/update_mapq.xml Thu May 24 11:51:27 2018 -0400 +++ b/update_mapq.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.11"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.12"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 5b8781514bc1 -r 6f9b1b81b593 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Thu May 24 11:51:27 2018 -0400 +++ b/write_supplementary_fastq.xml Fri Oct 26 06:11:17 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.11"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.12"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.11">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |