| Previous changeset 78:6178c24ddd5a (2020-04-07) Next changeset 80:c9361b7a025d (2020-04-07) |
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Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a" |
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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 6178c24ddd5a -r c42dd2551c9c add_matesequence.xml --- a/add_matesequence.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/add_matesequence.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.24"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.25"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6178c24ddd5a -r c42dd2551c9c allow_dovetailing.xml --- a/allow_dovetailing.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/allow_dovetailing.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.24"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.25"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 6178c24ddd5a -r c42dd2551c9c bam_readtagger.xml --- a/bam_readtagger.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/bam_readtagger.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.24"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.25"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r 6178c24ddd5a -r c42dd2551c9c extract_variants.xml --- a/extract_variants.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/extract_variants.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="extract_variants" name="Extract variant fragments" version="0.5.24"> +<tool id="extract_variants" name="Extract variant fragments" version="0.5.25"> <description>from long reads</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6178c24ddd5a -r c42dd2551c9c filter_insertions.xml --- a/filter_insertions.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/filter_insertions.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.24"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.25"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6178c24ddd5a -r c42dd2551c9c findcluster.xml --- a/findcluster.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/findcluster.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.24"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.25"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6178c24ddd5a -r c42dd2551c9c normalize_readsizes.xml --- a/normalize_readsizes.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/normalize_readsizes.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.24"> +<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.25"> <description>of multiple fastq files</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>normalize_readsizes --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6178c24ddd5a -r c42dd2551c9c plot_coverage.xml --- a/plot_coverage.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/plot_coverage.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.24"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.25"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re @@ -10,7 +10,7 @@ #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier)) --file '$r.input' '$identifier' $r.total_reads #end for -output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind +output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind --style $style ]]></command> <inputs> <repeat name="input_files" title="Add input files to coverage plot" min="1"> @@ -31,6 +31,29 @@ <option value="area">Area plot</option> <option value="line">Line plot</option> </param> + <param name="style" type="select" label="Select a plotting style"> + <option value="ggplot">ggplot</option> + <option value="classic">classic</option> + <option value="greyscale">greyscale</option> + <option value="dark_background">dark_background</option> + <option value="seaborn">seaborn</option> + <option value="seaborn-bright">seaborn-bright</option> + <option value="seaborn-colorblind">seaborn-colorblind</option> + <option value="seaborn-dark">seaborn-dark</option> + <option value="seaborn-dark-palette">seaborn-dark-palette</option> + <option value="seaborn-darkgrid">seaborn-darkgrid</option> + <option value="seaborn-deep">seaborn-deep</option> + <option value="seaborn-muted">seaborn-muted</option> + <option value="seaborn-notebook">seaborn-notebook</option> + <option value="seaborn-paper">seaborn-paper</option> + <option value="seaborn-pastel">seaborn-pastel</option> + <option value="seaborn-poster">seaborn-poster</option> + <option value="seaborn-talk">seaborn-talk</option> + <option value="seaborn-ticks">seaborn-ticks</option> + <option value="seaborn-white">seaborn-white</option> + <option value="seaborn-whitegrid">seaborn-whitegrid</option> + <option value="tableau-colorblind10">tableau-colorblind10</option> + </param> </inputs> <outputs> <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> |
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| diff -r 6178c24ddd5a -r c42dd2551c9c update_mapq.xml --- a/update_mapq.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/update_mapq.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.5.24"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.25"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6178c24ddd5a -r c42dd2551c9c write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Tue Apr 07 08:57:47 2020 -0400 +++ b/write_supplementary_fastq.xml Tue Apr 07 13:41:14 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.24"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.25"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.5.24">readtagger</requirement> + <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |