# HG changeset patch
# User eduardo
# Date 1438595044 14400
# Node ID 48006f05c208071acfd7eb6e7a7663b584ec8eaf
# Parent  a6bcb0f8f38e268570ac5e9d60ec6bddc5132f0c
Deleted selected files

diff -r a6bcb0f8f38e -r 48006f05c208 url2bowtie/download_align.xml
--- a/url2bowtie/download_align.xml	Mon Aug 03 05:43:47 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<tool id="download_align" name="Download and align" version="0.0.1">
-  <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description>
-  <requirements>
-      <requirement type="package" version="1.6">cutadapt</requirement>
-      <requirement type="package" version="2.2.4">bowtie2</requirement>
-      <requirement type="package" version="0.1.19">samtools</requirement>
-  </requirements>
-  <command>
-  #set index_path = ''
-  #if str($reference_genome.source) == "history":
-    echo \${PATH} &amp;&amp; bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
-    ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
-    #set index_path = 'genome'
-  #else:
-    #set index_path = $reference_genome.index.fields.path
-  #end if
-  wget -O - $file | gunzip -c | cutadapt   -q 20 - | bowtie2  -q 
-  ## index file path
-  -x $index_path 
-  -U - | samtools view -b - > $output
-  </command>
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Tool exception" />
-  </stdio>
-  <inputs>
-    <param format="text" name="file" type="text" label="URL for fastq.gz"/>
-    <conditional name="reference_genome">
-          <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
-            <option value="indexed">Use a built-in genome index</option>
-            <option value="history">Use a genome from the history and build index</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-              <options from_data_table="bowtie2_indexes">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>
-          <when value="history">
-            <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
-          </when>
-    </conditional>
-  </inputs> 
-  <outputs> 
-      <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)" />
-  </outputs>
-  <help>
-    This tool extracts reads from sra, runs cutdapt and bowtie and outputs a bam file. 
-
-    Contact Eduardo Alves at eduardoalves@abdn.ac.uk for support and bug reports.
-  </help>
-</tool>