diff galaxy-tools/biobank/utils/split_by_study.xml @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/split_by_study.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,42 @@
+<tool id="split_by_study"
+      name="VLUTIL.split_individuals_by_study"
+      force_history_refresh="true">
+
+    <description>
+        Split a file containing pedigree informations in multiple files using the study as split criteria
+    </description>
+
+    <command interpreter="bash">
+        launcher.sh
+        --interpreter=python
+        --runner=split_by_study.py
+        --in-file=${in_file}
+        --logfile=${log_file}
+        --record-id=$log_file.id
+        --out-path=$__new_file_path__
+    </command>
+
+    <inputs>
+        <param format="tabular" name="in_file" type="data"
+               label="input TSV file"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log_file"
+              label="${tool.name}.log"/>
+    </outputs>
+
+    <help>
+Split a file like::
+
+  individual    gender  father       mother
+  ASTUDY:2141   MALE    ASTUDY:12    ASTUDY:12341
+  ASTUDY:415    MALE    ASTUDY:3562  ASTUDY:13612
+  BSTUDY:12515  FEMALE  BSTUDY:3512  BSTUDY:124
+
+into multiple files based on the STUDY value of the label stored in the "individual" column.
+Each label in the "individual" column must have a STUDY:ENROLLMENT_CODE format, otherwise the line
+will be skipped.
+    </help>
+
+</tool>
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