# HG changeset patch
# User romaingred
# Date 1510908082 18000
# Node ID 928b9b0aa75b85a9c7372319a538900befff1abc
# Parent  a9fcdf7991b9337854313f2aff5855444dc99e0c
Uploaded

diff -r a9fcdf7991b9 -r 928b9b0aa75b alignTophat.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignTophat.xml	Fri Nov 17 03:41:22 2017 -0500
@@ -0,0 +1,151 @@
+<tool id="alignTophat" name="align RNAseq" version="0.0.1">
+  <description>Align directionnal RNAseq to obtain bedgraphs and raw count file</description>
+  <command interpreter="perl">
+    
+    ./alignTophat.pl
+    
+    --fastq ${first_input}
+    --fastq_n ${first_input.name}
+    
+    #if $Genome.refGenomeSource == "history":
+    --ref "${Genome.ownFile}"
+    --build_ref
+    #else:
+    --ref "${Genome.indices.fields.path}"
+    #end if
+    
+    #if $contaminants.refGenomeSource == "history":
+    --contaminants "${contaminants.ownFile}"
+    --build_contaminant
+    #else:
+    --contaminants "${contaminants.indices.fields.path}"
+    #end if
+    #if $anno.bedpipe == "history":
+      --anno "${anno.ownFile}"
+    #else:
+      --anno "${anno.indices.fields.path}"
+    #end if
+
+    --mis  $mis
+    --ma $ma
+    
+    --dirbam $dirbam
+    --dirbamCont $dirbamcont
+    --dirbedgraph $dirbedgraph
+    
+    --text $text
+    
+    --random_w $rand
+    --find $idDir.find
+    --direction $idDir.direc
+  </command>
+  <inputs>
+    
+    <param format="fastqsanger" name="first_input" type="data" label="fastq produced by fasteris" help=""/>
+    
+    
+    <conditional name="Genome">
+      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a reference genome">
+          <options from_data_table="bowtie2_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    
+    
+    <conditional name="Genome">
+      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a reference genome">
+          <options from_data_table="bowtie2_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    
+    <conditional name="contaminants">
+      <param name="refGenomeSource" type="select" label="Will you select contaminants database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select contaminants reference">
+          <options from_data_table="bowtie2_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    
+    <conditional name="anno">
+      <param name="bedpipe" type="select" label="Will you select an annotation file from your history or use a built-in index?" help="tab file format, (chr start end id score strand type description1 description2 description3">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select annotation file">
+          <options from_data_table="bed_pipe">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="bed" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    
+    
+    <param name="mis" type="integer" value="0" label="mismatches"/>
+    <param name="ma" type="integer" value="0" label="normalization value" help="e.g number of mappers (if 0 auto)"/> 
+    <param name="rand" type="boolean" checked="false" label="work on multi-mappers randomly assigned"/>
+
+
+    <conditional name="idDir">
+      <param name="direc" type="boolean" checked="true" label="directional library"/>
+      <when value="false">
+        <param name="find" type="hidden" value="false"/>
+      </when>
+      <when value="true">
+        <param name="find" type="boolean" checked="true" label="auto sens finder"/>
+      </when>
+     </conditional>
+  </inputs>
+  
+  <outputs>
+    <data format="tar" name="dirbam" label="alignement_zip_${first_input.name}"/>
+    <data format="tar" name="dirbamcont" label="contaminant_zip_${first_input.name}"/>
+    <data format="tar" name="dirbedgraph" label="bedgraph_zip_${first_input.name}"/>
+    <data format="tabular" name="text" label="raw_count_tabular_${first_input.name}_rand_${rand}"/>
+  </outputs>
+  
+  <requirements>
+    <requirement type="package" version="2.2.6">bowtie2</requirement>
+    <requirement type="package" version="2.1.0">tophat</requirement>
+    <requirement type="package" version="2.26.0">bedtools</requirement>
+    <requirement type="package" version="1.3.1">samtools</requirement>
+   </requirements>
+  
+</tool>