diff RM_custom_search.xml @ 0:a4cd8608ef6b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RM_custom_search.xml	Mon Apr 01 07:56:36 2019 -0400
@@ -0,0 +1,28 @@
+<tool id="RMsearch" name="RepeatMasker custom search" version="1.0.1">
+
+  <description>Scan clustering results using RepeatMasker against custom database of repeats</description>
+  <requirements>
+    <requirement type="package" version="4.0.7" >repeatmasker</requirement> 
+  </requirements>
+
+  <command interpreter="python3">
+    RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html
+  </command>
+
+  <inputs>
+    <param format="zip" type="data" name="input_zip" label="Input clustering data in as zip archive" help="zip archive obtained from previouse Graph-based sequence clustering"/>
+    <param name="RMdatabase" format="fasta" type="data" label="Library of repeats" help="Library of repeats as DNA sequences in fasta format. The recommended format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
+  </inputs>
+  
+  <outputs>
+    <data format="html" name="output_html" label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} " />
+  </outputs>
+
+  <help>
+    **What it does**
+
+    Use this tool if you want to scan previous clustering result with custom database of repeats using repeatmasker. 
+    
+  </help>
+</tool>
+