diff seq2HLA.xml @ 1:155b796033b6 draft default tip

Uploaded

--- a/seq2HLA.xml	Thu Dec 20 10:37:01 2012 -0500
+++ b/seq2HLA.xml	Fri Dec 21 03:46:15 2012 -0500
@@ -2,6 +2,7 @@
     <description>HLA typing from RNA-Seq sequence read</description>
     <command interpreter="python">
       seq2HLA.py
+      -t $threads
       -z $compressed
       -1 $readFile1
       -2 $readFile2
@@ -13,12 +14,13 @@
       -g $logfile
     </command>
     <inputs>
-      <param name="compressed" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Select if your input files are compressed gzipped fastq files" help="Leave default if you didn't upload the files or don't know"/>
+      <param name="compressed" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Select if your input files are compressed gzipped fastq files" help="Leave default (not checked) if you are unsure"/>
       <param format="fastq,fastqsanger" name="readFile1" type="data" label="Forward FASTQ File" help="FASTQ File with forward reads" />
       <param format="fastq,fastqsanger" name="readFile2" type="data" label="Reverse FASTQ File" help="FASTQ File with reverse reads" />
       <param name="runName" type="text" value="Run1" label="Run Name" help="Name of the Run" />
       <param name="readLength" type="integer" value="50" label="Read Length" help="Length of the input reads" />
       <param name="trim" type="integer" value="0" label="Trim x bases from the low quality 3' end" help="Trim x bases from the low quality 3' end. Default: 0" />
+      <param name="threads" type="integer" value="4" label="Number of threads to use for Bowtie" help="Choose a plausible amount of threads to use for Bowtie in this tool" />
     </inputs>
     <outputs>
       <data format="txt" name="out1" label="${tool.name} on ${on_string}: Output 1" />
@@ -33,6 +35,7 @@
 	<param name="runName" value="Run1"/>
 	<param name="readLength" value="37"/>
 	<param name="trim" value="0"/>
+	<param name="threads" value="4"/>
 	<output name="out1" file="output1.txt"/>
 	<output name="out2" file="output2.txt"/>
 	<output name="logfile" file="log.txt"/>
@@ -51,6 +54,11 @@
 
 .. class:: infomark
 
+**Dependencies**
+
+- bowtie
+- R
+
 **Input**
 
 Input files in FASTQ format
@@ -73,7 +81,7 @@
 
 -----
 
-.. image:: ./static/images/tron_logo.png
+.. image:: http://tron-mainz.de/wp-content/themes/tron/images/page_logo.png
 
 </help>
 </tool>