| Previous changeset 34:240c901dedc0 (2017-11-20) Next changeset 36:d0b3329a8e4b (2017-12-14) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh findcluster.xml plot_coverage.xml test-data/three_cluster_plot.pdf update_mapq.xml write_supplementary_fastq.xml |
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| diff -r 240c901dedc0 -r 02afdbc69591 add_matesequence.xml --- a/add_matesequence.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/add_matesequence.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.1"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.4"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 240c901dedc0 -r 02afdbc69591 allow_dovetailing.xml --- a/allow_dovetailing.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/allow_dovetailing.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.1"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.4"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 240c901dedc0 -r 02afdbc69591 bam_readtagger.xml --- a/bam_readtagger.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/bam_readtagger.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.1"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.4"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r 240c901dedc0 -r 02afdbc69591 findcluster.xml --- a/findcluster.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/findcluster.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.1"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.4"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -18,14 +18,14 @@ #if str($transposon_source.reference_source_selector) == "history": --transposon_reference_fasta '$transposon_source.ref_file' #else : - --transposon_bwa_index '$reference_source.ref_file.fields.path' + --transposon_bwa_index '$transposon_source.ref_file.fields.path' #end if #end if #if $genome_source.ref_file: #if str($genome_source.reference_source_selector) == "history": --genome_reference_fasta '$genome_source.ref_file' #else : - --genome_bwa_index '$reference_source.ref_file.fields.path' + --genome_bwa_index '$genome_source.ref_file.fields.path' #end if #end if --output_bam '$output_bam' |
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| diff -r 240c901dedc0 -r 02afdbc69591 plot_coverage.xml --- a/plot_coverage.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/plot_coverage.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.4.1"> +<tool id="plot_coverage" name="Plot coverage" version="0.4.4"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r 240c901dedc0 -r 02afdbc69591 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 240c901dedc0 -r 02afdbc69591 update_mapq.xml --- a/update_mapq.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/update_mapq.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.1"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.4"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 240c901dedc0 -r 02afdbc69591 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Mon Nov 20 10:50:42 2017 -0500 +++ b/write_supplementary_fastq.xml Thu Dec 14 03:52:04 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.1"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.4"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.1">readtagger</requirement> + <requirement type="package" version="0.4.4">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |