Mercurial > repos > mvdbeek > bam_tag_reads
changeset 0:66aa515e360e draft
planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit 2683c039c624b5231db2e76ae51cc13bf1e12f4e
| author | mvdbeek |
|---|---|
| date | Sun, 05 Feb 2017 14:27:17 -0500 |
| parents | |
| children | 8138277ea0e5 |
| files | bam_tag_reads.xml macros.xml test-data/dm6_a_pasteurianus.bam test-data/out.bam |
| diffstat | 4 files changed, 90 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_tag_reads.xml Sun Feb 05 14:27:17 2017 -0500 @@ -0,0 +1,61 @@ +<tool id="bam_tag_reads" name="Tag alignment files" version="0.1.2"> + <description>from multiple bam files</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.1.2">tag_reads</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + tag_reads -t '$tag_file' -a + #for $element in $alignment_series + '$element.annotate_with':$element.r_tag:$element.m_tag + #end for + -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> + </inputs> + <outputs> + <data name="tagged_file" format="bam"/> + </outputs> + <tests> + <test> + <param name="tag_file" value="dm6_a_pasteurianus.bam" ftype="bam"/> + <repeat name="alignment_series"> + <param name="annotate_with" value="dm6_a_pasteurianus.bam" ftype="bam"/> + <param name="r_tag" value="A"/> + <param name="m_tag" value="B"/> + </repeat> + <output name="tagged_file" file="out.bam" ftype="bam"/> + </test> + </tests> + <help><![CDATA[ + usage: tag_reads [-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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Feb 05 14:27:17 2017 -0500 @@ -0,0 +1,29 @@ +<macros> + <xml name="tag_options"> + <option value="A">A</option> + <option value="B">B</option> + <option value="C">C</option> + <option value="D">D</option> + <option value="E">E</option> + <option value="F">F</option> + <option value="G">G</option> + <option value="H">H</option> + <option value="I">I</option> + <option value="J">J</option> + <option value="K">K</option> + <option value="L">L</option> + <option value="M">M</option> + <option value="N">N</option> + <option value="O">O</option> + <option value="P">P</option> + <option value="Q">Q</option> + <option value="R">R</option> + <option value="S">S</option> + <option value="T">T</option> + <option value="U">U</option> + <option value="V">V</option> + <option value="W">W</option> + <option value="X">X</option> + <option value="Y">Y</option> + </xml> +</macros>