| Previous changeset 27:9f7737be4732 (2017-04-28) Next changeset 29:2c62ca47c455 (2017-05-09) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-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 9f7737be4732 -r be95c9c82937 add_matesequence.xml --- a/add_matesequence.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/add_matesequence.xml Tue May 09 10:38:06 2017 -0400 |
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| @@ -1,11 +1,11 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.21"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.22"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ - add_matesequence --file_to_annotate '$file_to_annotate' --annotate_source '$annotate_source' --output_path '$output' + add_matesequence --target '$file_to_annotate' --source '$annotate_source' --output_path '$output' ]]></command> <inputs> <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/> |
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| diff -r 9f7737be4732 -r be95c9c82937 allow_dovetailing.xml --- a/allow_dovetailing.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/allow_dovetailing.xml Tue May 09 10:38:06 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.21"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.22"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r 9f7737be4732 -r be95c9c82937 bam_readtagger.xml --- a/bam_readtagger.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/bam_readtagger.xml Tue May 09 10:38:06 2017 -0400 |
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| @@ -1,18 +1,18 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.21"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.22"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - readtagger -t '$tag_file' -a + readtagger -t '$tag_file' -s #for $element in $alignment_series '$element.annotate_with':$element.r_tag:$element.m_tag #end for $allow_dovetailing - $keep_suboptimal + $discard_suboptimal $discarded $verified $discard_proper_pairs @@ -30,11 +30,11 @@ <expand macro="tag_options"/> </param> </repeat> - <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/> - <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/> - <param argument="-dp" name="discard_proper_pairs" type="boolean" truevalue="-dp" falsevalue="" label="Discard alternative tags for proper pairs" help="Check this to discard alternative tags for reads in proper pairs"/> - <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/> - <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/> + <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"/> + <param argument="--discarded_path" name="discarded" type="boolean" truevalue="--discarded_path discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/> + <param argument="--verified_path" name="verified" type="boolean" truevalue="--verified_path verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/> </inputs> <outputs> <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/> |
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| diff -r 9f7737be4732 -r be95c9c82937 findcluster.xml --- a/findcluster.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/findcluster.xml Tue May 09 10:38:06 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.21"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.22"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 9f7737be4732 -r be95c9c82937 update_mapq.xml --- a/update_mapq.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/update_mapq.xml Tue May 09 10:38:06 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.21"> +<tool id="update_mapq" name="Update MAPQ score" version="0.3.22"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 9f7737be4732 -r be95c9c82937 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Fri Apr 28 02:16:42 2017 -0400 +++ b/write_supplementary_fastq.xml Tue May 09 10:38:06 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.21"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.22"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.21">readtagger</requirement> + <requirement type="package" version="0.3.22">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |