diff extract_files_from_re_archive.xml @ 17:d14b68e9fd1d draft

Uploaded - new tools added

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_files_from_re_archive.xml	Wed Apr 28 08:37:20 2021 +0000
@@ -0,0 +1,49 @@
+<tool id="extract_var_files_from_re" name="Extract various files from RepeatExplorer2 archive">
+  <command detect_errors="exit_code">
+
+    #for $sf in $file:
+
+    #if $sf == "CLUSTER_TABLE.csv"
+    unzip -p -j ${RepeatExplorer_archive} ${sf}  &gt; ${cluster_table}
+    ;
+    #end if
+
+    #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
+    unzip -p -j ${RepeatExplorer_archive} ${sf}  &gt; ${comparative_analysis_count}
+    ;
+    #end if
+
+    #if $sf == "SUPERCLUSTER_TABLE.csv"
+    unzip -p -j ${RepeatExplorer_archive} ${sf}  &gt; ${supercluster_table}
+    ;
+    #end if
+
+    #end for
+
+
+
+  </command>
+  
+  <inputs>
+    <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
+
+    <param name="file" type="select" label="select files you want to extract" multiple="true" optional="false">
+            <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option>
+            <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">COMPARATIVE_ANALYSIS_COUNTS.csv</option>
+            <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="cluster_table" label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}" >
+      <filter>"CLUSTER_TABLE.csv" in file</filter>
+    </data>
+    <data format="tabular" name="supercluster_table" label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
+      <filter>"SUPERCLUSTER_TABLE.csv" in file</filter>
+    </data>
+    <data format="tabular" name="comparative_analysis_count" label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}">
+      <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter>
+    </data>
+  </outputs>
+</tool>
+