diff makeTagDirectory.xml @ 2:7268cbc535e5 draft

findpeaks and maketagdirectory

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makeTagDirectory.xml	Fri Nov 23 00:30:27 2012 -0500
@@ -0,0 +1,48 @@
+<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="0.0.8">
+    <requirements>
+        <requirement type="package" >homer</requirement>
+    </requirements>
+    <description>makeTagDirectory</description>
+    <version_command>echo "Doh!"</version_command>
+    <command> makeTagDirectory ${tagDir.extra_files_path}
+        #for $alignF in $alignmentFiles
+          $alignF.file -format $alignF.file.ext
+        #end for
+        2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2
+
+    </command>
+    <inputs>
+        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
+        <repeat name="alignmentFiles" title="Alignment Files">
+          <param name="file" label="Add file" type="data" format="sam,bed" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="homerTagDirectory" name="tagDir" label="${title}" />
+        <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
+
+        After the job finishes, save the zip file, unzip and open "index.html"
+
+        The actual meme-chip command is displayed under "Command line summary"
+
+        Defaults:
+        http://meme.nbcr.net/meme/doc/meme-chip.html
+
+    </help>
+</tool>
+