changeset 1:6e90e7ad5e09 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_submit.xml	Tue Apr 10 15:54:25 2018 -0400
@@ -0,0 +1,42 @@
+<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
+    <description>Submits, checks for, and retrieves data for cancer annotation</description>
+  <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $output1 $output2 $output3 $output4</command>
+  
+  
+  <inputs>
+  
+    <param format="tabular" name="input" type="data" label="Source file"> </param>
+    <param format="tabular" name="dropdown" type="select" label="Analysis Program">
+      <option value="">None</option>
+      <option value="VEST">VEST</option>
+      <option value="CHASM">CHASM</option>
+      <option value="VEST;CHASM">VEST and CHASM</option>
+    </param>
+    <param format="tabular" name="GRCh" type="select" label="Genome Reference Consortium Human Build (GRCh)">
+      <option value="GRCh38">GRCh38/hg38</option>
+      <option value="GRCh37">GRCh37/hg19</option>
+    </param>
+    <param format="tabular" name="psm" type="data" optional="true" label="Peptide Spectrum Match Report (Optional)"> </param>
+    
+    
+  </inputs>
+  
+  <outputs>
+    <data format="cravat" label="CRAVAT: Variant Report" name="output1" />
+    <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="output2" />
+    <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="output3" />
+    <data format="cravat" label="CRAVAT: Errors" name="output4" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+  <help>
+ This tool submits, checks for, and retrieves data for cancer annotation from the CRAVAT platform at cravat.us.
+  </help>
+
+</tool>