# HG changeset patch
# User eugen
# Date 1344860478 14400
# Node ID 4d48b068b0b476cb9e5c69a183f2b48d69c8bcd2
# Parent  a6a7cf30cac784bece41db1af48c27e74ea99b3b
Deleted selected files

diff -r a6a7cf30cac7 -r 4d48b068b0b4 bismark.xml
--- a/bismark.xml	Mon Aug 13 08:12:54 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,181 +0,0 @@
-<tool id="bismark" name="Bismark Mapper" version="0.7.3">
-        <command interpreter="bash">
-               bismark_wrapper.sh
-			##Reference genome
-			ref="${indices.fields.path}"
-			##Output files (SAM output, Bismark summary)
-			mapped=$mapped
-			summary=$summary
-			##Temp directory
-			tempdir=$mapped.files_path
-			#if str($singlePaired.sPaired) == "single":
-			  library=single
-			  mate1=$singlePaired.sInput1
-			  #if $singlePaired.sParams.sSettingsType == "full":
-			    fullparam=true
-			    qual=$singlePaired.sParams.qual
-			    seedmms=$singlePaired.sParams.seedmms
-			    seedlen=$singlePaired.sParams.seedlen
-			    maqerr=$singlePaired.sParams.maqerr
-			    directional=$singlePaired.sParams.non_directional
-			    header=$singlePaired.sParams.sam_no_hd
-			  #end if
-			#else:
-			  library=paired
-			  mate1=$singlePaired.pInput1
-			  mate2=$singlePaired.pInput2
-			  #if $singlePaired.pParams.pSettingsType == "full":
-			    fullparam="true"
-			    qual=$singlePaired.pParams.qual
-			    seedmms=$singlePaired.pParams.seedmms
-			    seedlen=$singlePaired.pParams.seedlen
-			    maqerr=$singlePaired.pParams.maqerr
-			    directional=$singlePaired.pParams.non_directional
-			    header=$singlePaired.pParams.sam_no_hd
-			    minins=$singlePaired.pParams.minins
-			    maxins=$singlePaired.pParams.maxins
-			  #end if
-			#end if
-			
-			
-        </command>
-  <inputs>
-  <param name="indices" type="select" label="Select a reference genome">
-	        	<options from_data_table="bismark_bs_indeces">
-		        	<filter type="sort_by" column="2" />
-	                	<validator type="no_options" message="No indexes are available" />
-          		</options>
-  </param>
-  
-  <conditional name="singlePaired">
-      <param name="sPaired" type="select" label="Is this library mate-paired?">
-        <option value="single">Single-end</option>
-        <option value="paired">Paired-end</option>
-      </param>
-      <when value="single">
-        <param name="sInput1" type="data" format="fastq" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
-        <conditional name="sParams">
-          <param name="sSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
-            <option value="preSet">Commonly used</option>
-            <option value="full">Full parameter list</option>
-            </param>
-          <when value="preSet" />
-          <when value="full">
-	    <param name="qual" type="select" label="Select the type of FastQ qualities">
-		<option value="--phred33-quals">phred33-quals</option>
-		<option value="--phred64-quals">phred64-quals</option>
-		<option value="--solexa-quals">solexa-quals</option>
-	    </param>
-	    <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" />
-	    <param name="seedlen" type="integer" value="28" label="The seed length" />
-	    <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" />
-	    <param name="non_directional" type="select" label="Is the library a non-directional one?">
-	      <option value="">No</option>
-	      <option value="--non_directional">Yes</option>
-	    </param>
-	    <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?">
-	      <option value="">No</option>
-	      <option value="--sam-no-hd">Yes</option>
-	    </param>
-          </when> <!-- full -->
-        </conditional> <!-- sParams -->
-      </when> <!-- single -->
-   
-      <when value="paired">
-        <param name="pInput1" type="data" format="fastq" label="Forward FASTQ file" />
-	<param name="pInput2" type="data" format="fastq" label="Reverse FASTQ file" />
-
-        <conditional name="pParams">
-          <param name="pSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
-            <option value="preSet">Commonly used</option>
-            <option value="full">Full parameter list</option>
-          </param>
-          <when value="preSet" />
-          <when value="full">
-	    <param name="minins" type="integer" value="0" label="The minimum insert size for valid paired-end alignments" />
-	    <param name="maxins" type="integer" value="500" label="The maximum insert size for valid paired-end alignments" />
-	    <param name="qual" type="select" label="Select the type of FastQ qualities">
-		<option value="--phred33-quals">phred33-quals</option>
-		<option value="--phred64-quals">phred64-quals</option>
-		<option value="--solexa-quals">solexa-quals</option>
-	    </param>
-	    <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" />
-	    <param name="seedlen" type="integer" value="28" label="The seed length" />
-	    <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" />
-	    <param name="non_directional" type="select" label="Is the library a non-directional one?">
-	      <option value="">No</option>
-	      <option value="--non_directional">Yes</option>
-	    </param>
-	    <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?">
-	      <option value="">No</option>
-	      <option value="--sam-no-hd">Yes</option>
-	    </param>          
-          </when> <!-- full -->
-        </conditional> <!-- pParams -->
-      </when> <!-- paired -->
-    </conditional> <!-- singlePaired -->
-  
-  
- </inputs>
- <outputs>
-        <data name="mapped" format="sam" label="Bismark Mapped Reads" />
-	<data name="summary" format ="txt" label="Bismark Mapping Summary" />
- </outputs>
- <help>
-**What it does**
-
-Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are:
-
-   - Bisulfite mapping and methylation calling in one single step
-   
-   - Supports single-end and paired-end read alignments
-   
-   - Supports ungapped and gapped alignments
-   
-   - Alignment seed length, number of mismatches etc. are adjustable
-   
-   - Output discriminates between cytosine methylation in CpG, CHG and CHH context
-
-.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
-
-**Input formats**
-
-Bismark accepts files in Sanger FASTQ format.
-
-**Outputs**
-
-The output is in SAM format, and has the following columns::
-
-    Column  	Description
-  --------  	--------------------------------------------------------   
-  1 QNAME	seq-ID
-  2 FLAG 	this flag tries to take the strand a bisulfite read originated from into account (this is different from ordinary DNA alignment flags!)
-  3 RNAME 	chromosome
-  4 POS 	start position
-  5 MAPQ 	always 255
-  6 CIGAR
-  7 RNEXT
-  8 PNEXT
-  9 TLEN
- 10 SEQ
- 11 QUAL 	Phred33 scale
- 12 NM-tag 	edit distance to the reference
- 13 XX-tag 	base-by-base mismatches to the reference, not including indels
- 14 XM-tag 	methylation call string
- 15 XR-tag 	read conversion state for the alignment
- 16 XG-tag 	genome conversion state for the alignment
-   
- </help>
- 
- <tests>
-   <test>
-     <param name="sPaired" value="single" />
-     <param name="indices" value="bismark" />
-     <param name="sInput1" ftype="fastq" value="bismark_test_single.fastq" />
-     <param name="sParams" value="preSet" />
-     <output name="mapped" ftype="SAM" file="bismark_result_single_1.SAM" />
-     <ouput name="summary" ftype="txt" file="bismark_result_single_2.txt" />
-   </test>
- </tests>
-</tool>
-