# HG changeset patch
# User anmoljh
# Date 1440681376 14400
# Node ID 60d9e2097e026bb872877f6bb4a392b6cfab1cf7

Uploaded

diff -r 000000000000 -r 60d9e2097e02 insilico_read_normalization.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/insilico_read_normalization.xml	Thu Aug 27 09:16:16 2015 -0400
@@ -0,0 +1,157 @@
+<?xml version="1.0"?>
+<tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="r20140717">
+
+<!-- Written by Anmol J. Hemrom -->
+<description>Read Normalization</description>
+  
+    <requirements>
+        <requirement type="package" version="r20140717">trinityrnaseq</requirement>
+    </requirements>
+
+
+<command interperter="perl"> \$TRINITY_HOME/util/insilico_read_normalization.pl
+--JM $JM
+--max_cov $maximum_coverage
+
+## Inputs.
+#if str($inputs.paired_or_single) == "paired":
+
+        --left $inputs.left_input --right $inputs.right_input
+
+        #if  $inputs.left_input.ext == 'fa':
+                --seqType fa
+        #else:
+                --seqType fq
+        #end if
+
+        ## Additional parameters.
+        #if str($inputs.additional_params.use_additional) == "yes":
+
+                #if str($inputs.additional_params.library_type) != "None":
+                        --SS_lib_type $inputs.additional_params.library_type
+                #end if
+
+                $inputs.additional_params.pairs_together
+                --CPU $inputs.additional_params.CPU
+                $inputs.additional_params.PARALLEL_STATS
+                --KMER_SIZE $inputs.additional_params.KMER_SIZE
+                --max_pct_stdev $inputs.additional_params.max_pct_stdev
+
+        #end if
+
+
+#else:
+
+        --single $inputs.input
+
+        #if  str($inputs.input.ext) == 'fa':
+                --seqType fa
+        #else:
+                --seqType fq
+        #end if
+
+        ## Additional parameters.
+        #if str($inputs.additional_params.use_additional) == "yes":
+
+                #if str($inputs.additional_params.library_type) != "None":
+                        --SS_lib_type $inputs.additional_params.library_type
+                #end if
+
+                ##$inputs.additional_params.pairs_together
+                --CPU $inputs.additional_params.CPU
+                ##$inputs.additional_params.PARALLEL_STATS
+                --KMER_SIZE $inputs.additional_params.KMER_SIZE
+                --max_pct_stdev $inputs.additional_params.max_pct_stdev
+
+        #end if
+
+#end if
+
+
+
+## direct to output
+&gt; $insilico_read_normalization_log 2&gt;&amp;1
+
+</command>
+
+
+<inputs>
+        <param name="JM" type="select" label="JM" help="--JM &lt; string &gt; ; Amount of memory to allocate to Jellyfish for Kmer catalog construction">
+                <option value="1G">1G</option>
+                <option value="10G">10G</option>
+                <option value="20G">20G</option>
+                <option value="50G">50G</option>
+        </param>
+
+        <param name="maximum_coverage" type="integer" value="25" label="Maximum Coverage" help="--max_cov &lt; int &gt; ; targeted maximum coverage for reads"/>
+
+        <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=""/>
+
+                        <conditional name="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 value="yes">
+                                        <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="pairs_together" type="boolean" label="--pairs_together" help="process paired reads by averaging stats between pairs and retaining linking info" truevalue="--pairs_together" falsevalue="" checked="true" />
+                                        <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU &lt; int &gt; ; Number of CPUs to use (Maximum limit is 30 core)" />
+                                        <param name="PARALLEL_STATS" type="boolean" label="--PARALLEL_STATS"  help="Generate read stats in parallel for paired reads" truevalue="--PARALLEL_STATS" falsevalue="" checked="true" />
+                                        <param name="KMER_SIZE" type="integer"  value="25" label="--KMER SIZE" help="Default is 25" />
+                                        <param name="max_pct_stdev" type="integer"  value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/>
+                                </when>
+                        </conditional>
+                </when>
+
+
+                <when value="single">
+                        <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+
+                        <conditional name="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 value="yes">
+                                        <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>
+                                        <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU &lt; int &gt; ; Number of CPUs to use (Maximum limit is 30 core)" />
+                                        <param name="KMER_SIZE" type="integer"  value="25" label="--KMER SIZE" help="Default is 25" />
+                                        <param name="max_pct_stdev" type="integer"  value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/>
+                                </when>
+                        </conditional>
+                </when>
+        </conditional>
+
+
+</inputs>
+
+<outputs>
+	<data format="txt" name="insilico_read_normalization_log" label="${tool.name} on ${on_string}: log" />
+	<data format="fastq"  name="left_normalized_read"  label="${tool.name} on ${on_string}: Left  Read" from_work_dir="left.norm.fq"/>
+	<data format="fastq"  name="right_normalized_read" label="${tool.name} on ${on_string}: Right Read" from_work_dir="right.norm.fq"/>
+</outputs>
+
+
+<tests/>
+<help>Insilico Read Normalization</help>
+
+</tool>
+