| Previous changeset 43:6f9b1b81b593 (2018-10-26) Next changeset 45:d475729e90ea (2019-01-15) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit ae40519a953219ec4cc8ef4d586fc06cad88fb01 |
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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 6f9b1b81b593 -r 4870f1d6f037 add_matesequence.xml --- a/add_matesequence.xml Fri Oct 26 06:11:17 2018 -0400 +++ b/add_matesequence.xml Mon Jan 14 13:18:25 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.12"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.13"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.12">readtagger</requirement> + <requirement type="package" version="0.4.13">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 6f9b1b81b593 -r 4870f1d6f037 allow_dovetailing.xml --- a/allow_dovetailing.xml Fri Oct 26 06:11:17 2018 -0400 +++ b/allow_dovetailing.xml Mon Jan 14 13:18:25 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.12"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.13"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.12">readtagger</requirement> + <requirement type="package" version="0.4.13">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 6f9b1b81b593 -r 4870f1d6f037 bam_readtagger.xml --- a/bam_readtagger.xml Fri Oct 26 06:11:17 2018 -0400 +++ b/bam_readtagger.xml Mon Jan 14 13:18:25 2019 -0500 |
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| @@ -1,31 +1,31 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.13"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.12">readtagger</requirement> + <requirement type="package" version="0.4.13">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="qname_sorted.bam,bam"/> + <param name="tag_file" argument="--tag_file" type="data" format="bam"/> <repeat name="alignment_series" title="Alignments"> - <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/> + <param name="annotate_with" argument="--annotate_with" type="data" format="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 6f9b1b81b593 -r 4870f1d6f037 filter_insertions.xml --- a/filter_insertions.xml Fri Oct 26 06:11:17 2018 -0400 +++ b/filter_insertions.xml Mon Jan 14 13:18:25 2019 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.12"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.13"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.12">readtagger</requirement> + <requirement type="package" version="0.4.13">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><