# HG changeset patch
# User gkumar09
# Date 1443036102 14400
# Node ID 0fba4f817c44cb663381c332b5cfa0c9af41ddff
# Parent  a40a7ffdf14a7084b88841cd83d6f61e708c2eb8
Uploaded

diff -r a40a7ffdf14a -r 0fba4f817c44 alignreads.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignreads.xml	Wed Sep 23 15:21:42 2015 -0400
@@ -0,0 +1,138 @@
+<tool id="alignreads" name="alignReads" version="0.0.1">
+
+    <description>alignReads: short read alignment tool wrapper</description>
+    <requirements>
+        <requirement type="package">trinity</requirement>
+    </requirements>
+    <command interpreter="python">
+
+        trinityToolWrapper.py util/alignReads.pl --target $target -o alignment --aligner $aligner_selection.aligner
+
+
+        ## Inputs.
+        #if str($inputs.paired_or_single) == "paired":
+            --left $inputs.left_input --right $inputs.right_input
+            #if  $inputs.left_input.ext == 'fa':
+                --seqType fa
+            #else:
+                --seqType fq
+            #end if
+            #if str($inputs.library_type) != "None":
+                --SS_lib_type $inputs.library_type
+            #end if
+			--max_dist_between_pairs $inputs.max_dist_between_pairs
+        #else:
+            --single $inputs.input
+            #if  str($inputs.input.ext) == 'fa':
+                --seqType fa
+            #else:
+                --seqType fq
+            #end if
+            #if str($inputs.library_type) != "None":
+                --SS_lib_type $inputs.library_type
+            #end if
+        #end if
+
+        ## Additional parameters.
+	    ##if str($inputs.use_additional) == "yes":
+		##	-- $inputs.additional_params
+        ##end if
+	
+                
+        ## direct to output
+	    > outCapture.txt  
+
+
+    </command>
+    <inputs>
+		<param format="fasta" name="target" type="data" label="target" help="Fasta sequences targeted for short-read alignment"  />
+
+        <conditional name="inputs">
+		    <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+            </param>
+            <when value="paired">
+                <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+                <param name="library_type" type="select" label="Strand-specific Library Type">
+                    <option value="None">None</option>
+                    <option value="FR">FR</option>
+                    <option value="RF">RF</option>
+                </param>
+                <param name="max_dist_between_pairs" type="integer" value="2000" min="1" label="max_dist_between_pairs" help="Maximum length expected between fragment pairs as aligned to the target, including introns where relevant."/>
+
+
+            </when>
+            <when value="single">
+                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+                <param name="library_type" type="select" label="Strand-specific Library Type">
+                    <option value="None">None</option>
+                    <option value="F">F</option>
+                    <option value="R">R</option>
+                </param>
+            </when>
+        </conditional>
+
+		<conditional name="aligner_selection">
+			<param name="aligner" type="select" label="Select alignment tool to run">
+				<option value="bowtie">bowtie</option>
+				<option value="bwa">bwa</option>
+				<option value="blat">blat</option>
+			</param>
+			<when value="blat">
+				<param name="max_intron_length" type="integer" value="10000" min = "1" label="maximum intron length" help="" />
+				<param name="min_percent_identity" type="integer" value="95" min="1" label="minimum percent identity" help="" />
+			</when>
+			<when value="bwa">
+			</when>
+			<when value="bowtie">
+			</when>
+		</conditional>
+
+
+	<!--	    	
+		<conditional name="use_additional_params">
+            <param name="use_additional" type="select" label="Use Additional Params?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">            
+				<param name="additional_params" type="text" value="" label="Additional command-line parameters to aligner" help="" />
+            </when>
+        </conditional>
+    
+	-->
+
+    </inputs>
+    <outputs>
+        <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: COORD-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>
+		<data format="bam" name="nameSortedBam" label="${tool.name} on ${on_string}: NAME-sorted read alignments" from_work_dir="alignment/alignment.nameSorted.bam"/>
+
+		<!-- notes: need to retain:
+			 -the sample name for the alignment
+			 -coordinate-sorted vs. name-sorted bam file
+			 -paired vs. unpaired vs. strictly proper pairs (for RSEM)
+			 -strand-specific or not
+		-->
+
+	</outputs>
+    <tests>
+
+
+		<test>
+			<param name="target" value="trinity/Trinity.fasta" />
+			<param name="aligner" value="bowtie" />
+			<param name="paired_or_single" value="single" />
+			<param name="library_type" value="None" />
+			<param name="input" value="trinity/reads.left.fq" />
+        </test>
+	
+
+    </tests>
+    <help>
+        .. _Trinity: http://trinityrnaseq.sourceforge.net
+    </help>
+</tool>