# HG changeset patch
# User romaingred
# Date 1510907655 18000
# Node ID 1b586f3740a1c5383ee9a373cbd879b462ff9427
# Parent  411b36116b7af334099a01ba4c4c2916e04e7e26
Deleted selected files

diff -r 411b36116b7a -r 1b586f3740a1 alignTophat.xml
--- a/alignTophat.xml	Fri Nov 17 03:34:12 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,151 +0,0 @@
-<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 $anno.bedpipe == "history":
-      --annot "${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="2.17.0">bedtools</requirement>
-    <requirement type="package" version="0.1.19">samtools</requirement>
-   </requirements>
-  
-</tool>