| Previous changeset 77:b9b76f9a816c (2020-03-24) Next changeset 79:c42dd2551c9c (2020-04-07) |
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Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013" |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh extract_variants.xml filter_insertions.xml findcluster.xml normalize_readsizes.xml plot_coverage.xml test-data/three_cluster_plot.pdf update_mapq.xml write_supplementary_fastq.xml |
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added:
test-data/three_cluster_plot_line.pdf |
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| diff -r b9b76f9a816c -r 6178c24ddd5a add_matesequence.xml --- a/add_matesequence.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/add_matesequence.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.23"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.24"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a allow_dovetailing.xml --- a/allow_dovetailing.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/allow_dovetailing.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.23"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.24"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r b9b76f9a816c -r 6178c24ddd5a bam_readtagger.xml --- a/bam_readtagger.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/bam_readtagger.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.23"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.24"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r b9b76f9a816c -r 6178c24ddd5a extract_variants.xml --- a/extract_variants.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/extract_variants.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="extract_variants" name="Extract variant fragments" version="0.5.23"> +<tool id="extract_variants" name="Extract variant fragments" version="0.5.24"> <description>from long reads</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a filter_insertions.xml --- a/filter_insertions.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/filter_insertions.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.23"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.24"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a findcluster.xml --- a/findcluster.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/findcluster.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.23"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.24"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a normalize_readsizes.xml --- a/normalize_readsizes.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/normalize_readsizes.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.23"> +<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.24"> <description>of multiple fastq files</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>normalize_readsizes --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a plot_coverage.xml --- a/plot_coverage.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/plot_coverage.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.23"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.24"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">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' +output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind ]]></command> <inputs> <repeat name="input_files" title="Add input files to coverage plot" min="1"> @@ -27,6 +27,10 @@ </valid> </sanitizer> </param> + <param name="plot_kind" type="select" label="Select the plot type"> + <option value="area">Area plot</option> + <option value="line">Line plot</option> + </param> </inputs> <outputs> <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> @@ -40,6 +44,15 @@ <param name="regions" value="3R:13373525-13373615"/> <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> </test> + <test> + <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/> + <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/> + <param name="input_files_0|total_reads" value="1000000" ftype="bam"/> + <param name="input_files_1|total_reads" value="1000000" ftype="bam"/> + <param name="regions" value="3R:13373525-13373615"/> + <param name="plot_kind" value="line"/> + <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a test-data/three_cluster_plot.pdf |
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| Binary file test-data/three_cluster_plot.pdf has changed |
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| diff -r b9b76f9a816c -r 6178c24ddd5a test-data/three_cluster_plot_line.pdf |
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| Binary file test-data/three_cluster_plot_line.pdf has changed |
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| diff -r b9b76f9a816c -r 6178c24ddd5a update_mapq.xml --- a/update_mapq.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/update_mapq.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.5.23"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.24"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r b9b76f9a816c -r 6178c24ddd5a write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Tue Mar 24 07:23:30 2020 -0400 +++ b/write_supplementary_fastq.xml Tue Apr 07 08:57:47 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.23"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.24"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.5.23">readtagger</requirement> + <requirement type="package" version="0.5.24">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |