# HG changeset patch
# User geoffrey.dintilhac
# Date 1576951233 18000
# Node ID fef10ad6ee1569844313e51e1135f659ff0f4e45
# Parent  68f7b5a4b1e2c7f6cb00d68f5b264fa37c96a565
Uploaded

diff -r 68f7b5a4b1e2 -r fef10ad6ee15 bamtobed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtobed.xml	Sat Dec 21 13:00:33 2019 -0500
@@ -0,0 +1,116 @@
+ <tool id="bam_to_bed_convert" name="BAM-to-BED" version="1.0"> <!-- tool's name displayed on Galaxy --> 
+      <description>converter</description>
+      
+      <requirements> <!-- package required -->
+		  <requirement type="package" version="2.29.0">bedtools</requirement>
+	  </requirements>
+      
+      <command interpreter="python">bamtobed.py
+      -i $input 
+      -o $output
+      -oot $conditional.selector
+			
+      #if $conditional.selector =="Y":
+			-f $conditional.format_output_chosen
+      #end if
+      
+      -sc $score_calcul_selector.score_calcul_BED
+      #if $score_calcul_selector.score_calcul_BED =="tag":
+			-tag $score_calcul_selector.calcul_BED_tag
+      #end if
+      
+      #if $split_boolean =="Y":
+			-spt
+      #end if
+      
+      #if $cigar_boolean =="Y":
+			-cgr
+      #end if
+      </command>
+
+
+      <inputs>
+		  
+		  <param format="bam" name="input" type="data" label="Source file"/> <!-- input file -->
+
+        <conditional name="conditional"> <!-- Output file format different from BED ? -->	 
+			<param name="selector" type="select" label="Output file format different from BED">
+				<option value="N">No</option>
+				<option value="Y">Yes</option>
+			</param>
+			
+	
+
+			<when value="N"/>
+			<when value="Y"> <!-- format output chosen = not BED -->
+				<param name="format_output_chosen" type="select" label="Output file format chosen" help="use BEDPE only with paired-end input (and sorted by read name) dataset"> <!-- choice of output file format -->
+					<option value="BEDPE">BEDPE : add fields (chrom2, star2, end2, strand2) for paired-end sequence alignments</option> 
+					<option value="BED12">BED12 : each feature is described by all 12 columns</option>
+				</param>	
+			</when>
+		</conditional> 	
+		
+		<conditional name="score_calcul_selector"> <!-- choice of the score calculation -->
+             <param name="score_calcul_BED" type="select" label="Select a calculation for BED score">
+				<option value="mapq">Use mapping quality (default)</option>
+				<option value="ed">Use alignment's edit-distance for BED score</option>
+				<option value="tag">Use other BAM alignment tag for BED score</option>
+			</param>
+			<when value="tag">
+				<param name="calcul_BED_tag" type="text" label="Enter other BAM alignment tag as the BED score" help ="/!\ Choice of another tag for score calculation is disallowed with BEDPE output /!\"/>
+			</when>
+		</conditional>
+		
+		<!-- option split and cigar : -->
+		<param name="split_boolean" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="To split or not to split ?" help="Report each portion of a “split” BAM while obeying both “N” CIGAR and “D” operation. Be careful : -split is disallowed with edit-distance as a calculation for BED score."></param>
+		<param name="cigar_boolean" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="CIGAR string ?" help="Add the CIGAR string to the BED entry as a 7th column. Be careful : -cigar is not displayed with -splits, and disallowed with edit-distance as a calculation for BED score."></param>
+
+      </inputs>						
+
+     
+      <outputs>
+        <data format="bed" name="output"/>
+      </outputs>
+
+
+     <tests>
+       <test>
+         <param name="input" value="bam_to_bed_convert.bam"/>
+         <output name="out_file" file="bam_to_bed_convert.bed"/>
+       </test>
+     </tests>
+   
+   
+     <help>
+**What it does**: this tool converts sequence alignments in BAM format into BED, BED12 or BEDPE format running the command "bamtobed" of bedtools. 
+
+.. class:: warningmark
+
+If you want a **BEDPE output**, your input has to be paired-end and sorted by read name.
+
+.. class:: warningmark
+
+About **score calculation** : the option "another tag" is disallowed with BEDPE output.
+
+.. class:: warningmark
+
+About the options **-split** and **-cigar** : -split is disallowed with edit-distance as a calculation for BED score. -cigar is not displayed with -splits, and disallowed with edit-distance as a calculation for BED score.
+
+.. class:: infomark
+
+For more information, please refer to this link : https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at https://toolshed.g2.bx.psu.edu/view/geoffrey.dintilhac/bam_to_bed/68f7b5a4b1e2
+
+**If you use this tool in Galaxy, please cite:**
+
+     </help>
+     
+    <citations>
+		<citation type="doi">10.1093/bioinformatics/btq033</citation>
+	</citations>
+   
+</tool>
+
+