| Previous changeset 28:be95c9c82937 (2017-05-09) Next changeset 30:db5c766503dd (2017-05-11) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml update_mapq.xml write_supplementary_fastq.xml |
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| diff -r be95c9c82937 -r 2c62ca47c455 add_matesequence.xml --- a/add_matesequence.xml Tue May 09 10:38:06 2017 -0400 +++ b/add_matesequence.xml Tue May 09 12:54:10 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.22"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.23"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.22">readtagger</requirement> + <requirement type="package" version="0.3.23">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r be95c9c82937 -r 2c62ca47c455 allow_dovetailing.xml --- a/allow_dovetailing.xml Tue May 09 10:38:06 2017 -0400 +++ b/allow_dovetailing.xml Tue May 09 12:54:10 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.22"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.23"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.22">readtagger</requirement> + <requirement type="package" version="0.3.23">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r be95c9c82937 -r 2c62ca47c455 bam_readtagger.xml --- a/bam_readtagger.xml Tue May 09 10:38:06 2017 -0400 +++ b/bam_readtagger.xml Tue May 09 12:54:10 2017 -0400 |
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| @@ -1,16 +1,19 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.22"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.23"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.22">readtagger</requirement> + <requirement type="package" version="0.3.23">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 @@ -30,6 +33,7 @@ <expand macro="tag_options"/> </param> </repeat> + <param argument="--reference_fasta" type="data" format="fasta" label="Reference fasta for realigning clipped reads" optional="True" help="This file is optional. If you provide it, clipped sequences are extracted and aligned against this fasta file."/> <param argument="--allow_dovetailing" type="boolean" truevalue="--allow_dovetailing" falsevalue="--no_allow_dovetailing" checked="True" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/> <param argument="--discard_suboptimal_alternate_tags" name="discard_suboptimal" type="boolean" checked="True" truevalue="--discard_suboptimal_alternate_tags" falsevalue="--no_discard_suboptimal" label="Discard suboptimal alternative tags" help="Check this to discard alternative tags that cannot explain the current read cigar"/> <param argument="--discard_if_proper_pair" name="discard_proper_pairs" type="boolean" truevalue="--discard_if_proper_pair" falsevalue="--no_discard_if_proper_pair" label="Discard alternative tags for proper pairs" checked="True" help="Check this to discard alternative tags for reads in proper pairs"/> |
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| diff -r be95c9c82937 -r 2c62ca47c455 findcluster.xml --- a/findcluster.xml Tue May 09 10:38:06 2017 -0400 +++ b/findcluster.xml Tue May 09 12:54:10 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.22"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.23"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.22">readtagger</requirement> + <requirement type="package" version="0.3.23">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r be95c9c82937 -r 2c62ca47c455 update_mapq.xml --- a/update_mapq.xml Tue May 09 10:38:06 2017 -0400 +++ b/update_mapq.xml Tue May 09 12:54:10 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.22"> +<tool id="update_mapq" name="Update MAPQ score" version="0.3.23"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.22">readtagger</requirement> + <requirement type="package" version="0.3.23">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r be95c9c82937 -r 2c62ca47c455 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Tue May 09 10:38:06 2017 -0400 +++ b/write_supplementary_fastq.xml Tue May 09 12:54:10 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.22"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.23"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.22">readtagger</requirement> + <requirement type="package" version="0.3.23">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |