Mercurial > repos > mvdbeek > bam_readtagger
diff bam_readtagger.xml @ 0:a38447a59412 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
author | mvdbeek |
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date | Fri, 17 Feb 2017 10:54:47 -0500 |
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children | f69131f584e8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_readtagger.xml Fri Feb 17 10:54:47 2017 -0500 @@ -0,0 +1,92 @@ +<tool id="bam_readtagger" name="Tag alignment files" version="0.1.8"> + <description>from multiple bam files</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.1.8">readtagger</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + readtagger -t '$tag_file' -a + #for $element in $alignment_series + '$element.annotate_with':$element.r_tag:$element.m_tag + #end for + $allow_dovetailing + $keep_suboptimal + $discarded + $verified + -o '$tagged_file' + ]]></command> + <inputs> + <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="bam"/> + <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> + <expand macro="tag_options"/> + </param> + <param type="select" name="m_tag" label="First letter to use for mate tag" value="B"> + <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="-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> + <outputs> + <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/> + <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string"> + <filter>verified is True</filter> + </data> + <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string"> + <filter>verified is True</filter> + </data> + </outputs> + <tests> + <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) --> + <param name="tag_file" value="dm6.bam" ftype="bam"/> + <repeat name="alignment_series"> + <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/> + <param name="r_tag" value="A"/> + <param name="m_tag" value="B"/> + </repeat> + <param name="discarded" value="True"/> + <param name="verified" value="True"/> + <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/> + <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/> + <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/> + </test> + <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) --> + <param name="tag_file" value="pasteurianus.bam" ftype="bam"/> + <repeat name="alignment_series"> + <param name="annotate_with" value="dm6.bam" ftype="bam"/> + <param name="r_tag" value="A"/> + <param name="m_tag" value="B"/> + </repeat> + <param name="discarded" value="True"/> + <param name="verified" value="True"/> + <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" /> + <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> + </tests> + <help><![CDATA[ + usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o + OUTPUT_FILE + +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) + + ]]></help> +</tool>