diff findPeaks.xml @ 4:74c1fc7bb164 draft

display tag directories with html

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findPeaks.xml	Tue Nov 27 02:34:33 2012 -0500
@@ -0,0 +1,52 @@
+<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.0">
+    <requirements>
+        <requirement type="package">homer</requirement>
+    </requirements>
+    <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description>
+    <!--<version_command></version_command>-->
+    <command>
+        findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
+
+    #if $control_tagDir:
+        -i $control_tagDir.extra_files_path
+    #end if
+
+        2&gt; $out_log || echo "Error running findPeaks." >&amp;2
+    </command>
+    <inputs>
+        <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" />
+        <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" />
+        <param type="text" name="options" label="Extra options" value="" >
+          <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+          </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
+        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
+    </outputs>
+    <tests>
+        <test>
+            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
+            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
+        </test>
+    </tests>
+
+    <help>
+
+  .. class:: infomark
+
+  **Homer findPeaks**
+  http://biowhat.ucsd.edu/homer/ngs/peaks.html
+
+    </help>
+</tool>
+