Mercurial > repos > mvdbeek > bam_readtagger
changeset 3:cb9036583afe draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
| author | mvdbeek |
|---|---|
| date | Tue, 21 Feb 2017 04:39:31 -0500 |
| parents | 39d9bc17ec74 |
| children | 7625c594bc37 |
| files | add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml test-data/dm6_mate_annotated.bam test-data/proper_pair_discard.bam test-data/proper_pair_discard_fbti.bam test-data/proper_pair_discard_out.bam test-data/proper_pair_discard_verified_empty.bam test-data/proper_pair_out_suboptimal_tags.bam |
| diffstat | 9 files changed, 113 insertions(+), 27 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_matesequence.xml Tue Feb 21 04:39:31 2017 -0500 @@ -0,0 +1,45 @@ +<tool id="add_matesequence" name="Add matesequence" version="0.2.0"> + <description>into tag field</description> + <requirements> + <requirement type="package" version="0.2.0">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' + ]]></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"/> + <param name="annotate_source" argument="--annotate_source" label="Use this file to find the mate sequence (can be same file as file_to_annotate)" type="data" format="bam"/> + <param name="mate_sequence_tag" type="text" value="MS"/> + </inputs> + <outputs> + <data name="output" format="bam" label="Add matesequence on $on_string"/> + </outputs> + <tests> + <test> + <param name="file_to_annotate" value="dm6.bam" ftype="bam"/> + <param name="annotate_source" value="dm6.bam" ftype="bam"/> + <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +.. code-block:: + + usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o + OUTPUT_PATH [--version] + + Annotate reads with Mate Sequence in tag field + + optional arguments: + -h, --help show this help message and exit + -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE + Annotate reads in this file with their mate sequence + -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE + Use this file to find the mate sequence (can be same + file as file_to_annotate) + -o OUTPUT_PATH, --output_path OUTPUT_PATH + Write resulting BAM file to this path + --version show program's version number and exit + + ]]></help> +</tool>
--- a/allow_dovetailing.xml Fri Feb 17 12:55:58 2017 -0500 +++ b/allow_dovetailing.xml Tue Feb 21 04:39:31 2017 -0500 @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.1.13"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.2.0"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.1.13">readtagger</requirement> + <requirement type="package" version="0.2.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' @@ -19,16 +19,17 @@ </test> </tests> <help><![CDATA[ -:: -usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH +.. code-block:: -Allow dovetailing. + usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH + + Allow dovetailing. -optional arguments: - -h, --help show this help message and exit - -i INPUT_PATH, --input_path INPUT_PATH - Input alignment file to manipulate - -o OUTPUT_PATH, --output_path OUTPUT_PATH - Output alignment file + optional arguments: + -h, --help show this help message and exit + -i INPUT_PATH, --input_path INPUT_PATH + Input alignment file to manipulate + -o OUTPUT_PATH, --output_path OUTPUT_PATH + Output alignment file ]]></help> </tool>
--- a/bam_readtagger.xml Fri Feb 17 12:55:58 2017 -0500 +++ b/bam_readtagger.xml Tue Feb 21 04:39:31 2017 -0500 @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.1.13"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.2.0"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.1.13">readtagger</requirement> + <requirement type="package" version="0.2.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a @@ -15,6 +15,7 @@ $keep_suboptimal $discarded $verified + $discard_proper_pairs -o '$tagged_file' ]]></command> <inputs> @@ -30,6 +31,7 @@ </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"/> </inputs> @@ -69,24 +71,62 @@ <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/> <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/> </test> + <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair --> + <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/> + <repeat name="alignment_series"> + <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/> + <param name="r_tag" value="A"/> + <param name="m_tag" value="B"/> + </repeat> + <param name="discarded" value="True"/> + <param name="keep_suboptimal" value="True"/> + <param name="discard_proper_pairs" value="True"/> + <param name="verified" value="True"/> + <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" /> + <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/> + <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/> + </test> </tests> <help><![CDATA[ - usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o - OUTPUT_FILE +.. code-block:: -Tag reads in an alignment file based on other alignment files + usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o + OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED] + [-wv WRITE_VERIFIED] [--version] + + Tag reads in an alignment file based on other alignment files -optional arguments: - -h, --help show this help message and exit - -t TAG_FILE, --tag_file TAG_FILE - Tag reads in this file. (default: None) - -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...] - Tag reads in readfile if reads are aligned in these - files.Append `:A:B` to tag first letter of tag - describing read as A, and first letter of tag - describing the mate as B (default: None) - -o OUTPUT_FILE, --output_file OUTPUT_FILE - Write bam file to this path (default: None) + optional arguments: + -h, --help show this help message and exit + -t TAG_FILE, --tag_file TAG_FILE + Tag reads in this file. (default: None) + -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...] + Tag reads in readfile if reads are aligned in these + files.Append `:A:B` to tag first letter of tag + describing read as A, and first letter of tag + describing the mate as B (default: None) + -o OUTPUT_FILE, --output_file OUTPUT_FILE + Write bam file to this path (default: None) + -d, --allow_dovetailing + Sets the proper pair flag (0x0002) to true if reads + dovetail [reads reach into or surpass the mate + sequence]. (default: False) + -dp, --discard_if_proper_pair + Discard an alternative flag if the current read is in + a proper pair. (default: False) + -k, --keep_suboptimal_alternate_tags + By default cigarstrings of the alternative tags are + compared and alternates that are not explaining the + current cigar strings are discarded. Use this option + to keep the alternative tags (effectively restoring + the behaviour of readtagger < 0.1.4) (default: False) + -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED + Write discarded reads into separate file (default: + False) + -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED + Write verified reads into separate file (default: + False) + --version show program's version number and exit ]]></help> </tool>