diff makeTagDirectory.xml @ 10:7efeace8bd32 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makeTagDirectory.xml	Mon Dec 17 00:22:39 2012 -0500
@@ -0,0 +1,61 @@
+<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
+    <requirements>
+        <requirement type="package" >homer</requirement>
+    </requirements>
+    <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description>
+    <!--<version_command></version_command>-->
+    <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} 
+        #for $alignF in $alignmentFiles
+          $alignF.file -f $alignF.file.ext
+        #end for
+          -o $tagDir
+        2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2
+
+    </command>
+    <inputs>
+        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
+        <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
+          <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+             <remove value="/"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+          </sanitizer>
+        </param>
+        <repeat name="alignmentFiles" title="Alignment Files">
+          <param name="file" label="Add file" type="data" format="sam,bed" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
+        <data format="html" name="tagDir" label="${title} tag directory" />
+        <data format="txt" name="out_log" label="${title}.log" />
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+    </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 makeTagDirectory**
+
+  For more options, look under: "Command line options"
+
+  http://biowhat.ucsd.edu/homer/ngs/tagDir.html
+
+
+    </help>
+</tool>
+