Mercurial > repos > iuc > bctools_extract_alignment_ends
diff extract_aln_ends.xml @ 0:0e70f9058b02 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author | iuc |
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date | Tue, 14 Nov 2017 05:53:02 -0500 |
parents | |
children | 0be29a221b16 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_aln_ends.xml Tue Nov 14 05:53:02 2017 -0500 @@ -0,0 +1,49 @@ +<tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@VERSION@"> + <description>from SAM or BAM</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + extract_aln_ends.py + '$alignments' + > '$alignment_ends' + ]]></command> + <inputs> + <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/> + </inputs> + <outputs> + <data name="alignment_ends" format="bed"/> + </outputs> + <tests> + <test> + <param name="alignments" value="twomates.sam"/> + <output name="alignment_ends" file="tworeads_aln_ends.bed"/> + </test> + </tests> + <help><![CDATA[ + +bctools - Extract alignment ends from from SAM or BAM alignments +================================================================ + +The resulting BED file contains the outer coordinates of the alignments. The BED +name field is set to the read id and the score field is set to the edit distance +of the alignment. The crosslinked nucleotide is one nt upstream of the 5'-end of +the BED entries. + +This tool only reports results for alignments that are properly aligned in FR +("forward-reverse") direction. + +Input: +------ + +* BAM file containing alignments (paired-end sequencing) + +Output: +------- + +* BED file containing outer coordinates (sorted by read id) + + ]]></help> + <expand macro="citations"/> +</tool>