diff sailfish.xml @ 0:2306a9c40c37 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sailfish.xml	Sat Jul 12 03:28:47 2014 -0400
@@ -0,0 +1,81 @@
+<tool id="sailfish" name="Sailfish" version="0.6.3.0">
+    <description>transcript quantification from RNA-seq data</description>
+    <version_command>sailfish -version</version_command>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        sailfish quant -i $index_dir 
+            #if $single_or_paired-single_or_paired_opts == 'single':
+                -l "TYPE=SE"
+                -r $single_or_paired_opts.input_singles
+            #else:
+                -1 $single_or_paired_opts.input_mate1
+                -2 $single_or_paired_opts.input_mate2
+                #if $single_or_paired_opts.orientation == "same":
+                    -l "TYPE=PE:O=>>"
+                #elif $single_or_paired_opts.orientation == "away":
+                    -l "TYPE=PE:O=<>"
+                #else:
+                    -l "TYPE=PE:O=><"
+                #end if
+            #end if
+-o <quant_dir>
+
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <conditional name="single_or_paired">
+            <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
+            </when>
+            <when value="paired">
+                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." />
+                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." />
+                <param name="orientation" type="select" label="Relative orientation of reads within a pair">
+                    <option value="same">Mates are oriented in the same direction</option>
+                    <option value="away">Mates are oriented away from each other</option>
+                    <option value="toward" selected="True">Mates are oriented toward each other</option>
+                </param>
+            </when>
+        </conditional>
+
+        <expand macro="input_conditional_index" />
+
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
+            <expand macro="output_change_format" />
+        </data>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+
+The first option >> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is 
+upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa.
+
+The second option &lt;&gt; denotes that the mates are oriented away from each other. This implies that start 
+of mate1 is closer to start of mate 2 than the end of mate 2, etc.
+
+The third option &gt;&lt; is, perhaps, the most common relative orientation. It denotes that the mates are 
+oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa.
+
+-------
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following:
+
+
+]]>
+    </help>
+</tool>