| Previous changeset 51:08656cd6c989 (2019-02-15) Next changeset 53:5eb0ec276ea5 (2019-06-13) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 45d0337e2a0d35e9a83d9c87c005c876c45ee054 |
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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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removed:
test-data/extended_and_annotated_roi.bam.bai test-data/out.png test-data/three_cluster_out.bam.bai |
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| diff -r 08656cd6c989 -r b03c6d8c37c1 add_matesequence.xml --- a/add_matesequence.xml Fri Feb 15 02:31:18 2019 -0500 +++ b/add_matesequence.xml Wed Jun 12 14:23:52 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.19"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.0"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.19">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 08656cd6c989 -r b03c6d8c37c1 allow_dovetailing.xml --- a/allow_dovetailing.xml Fri Feb 15 02:31:18 2019 -0500 +++ b/allow_dovetailing.xml Wed Jun 12 14:23:52 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.19"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.0"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.19">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 08656cd6c989 -r b03c6d8c37c1 bam_readtagger.xml --- a/bam_readtagger.xml Fri Feb 15 02:31:18 2019 -0500 +++ b/bam_readtagger.xml Wed Jun 12 14:23:52 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.19"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.0"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.19">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r 08656cd6c989 -r b03c6d8c37c1 filter_insertions.xml --- a/filter_insertions.xml Fri Feb 15 02:31:18 2019 -0500 +++ b/filter_insertions.xml Wed Jun 12 14:23:52 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.19"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.0"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.19">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -20,9 +20,9 @@ $output_discard ]]></command> <inputs> - <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> - <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> - <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> + <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/> + <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> + <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/> </inputs> <outputs> |
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| diff -r 08656cd6c989 -r b03c6d8c37c1 findcluster.xml --- a/findcluster.xml Fri Feb 15 02:31:18 2019 -0500 +++ b/findcluster.xml Wed Jun 12 14:23:52 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.19"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.0"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.19">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><