diff validate_affy_metadata.xml @ 0:80d672b3e6dd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/validate_affy_metadata.xml	Thu Aug 15 13:17:41 2019 -0400
@@ -0,0 +1,75 @@
+<tool id="validate_affy_metadata" name="Validate Affymetrix metadata" version="1.0.0">
+    <description>for 96 well plate</description>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/validate_affy_metadata.py'
+--input '$input'
+--output '$output']]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Affymetrix 96 well plate metadata file">
+            <validator type="expression" message="96 well plate data must have 32 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==32 and value.metadata.data_lines<=96]]></validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="affy_metadata.tabular" ftype="tabular"/>
+            <output name="output" file="affy_metadata.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Validates an Affymetrix metadata file for 96 well plate data.  These files consist of 32 columns and no more than 96 data lines.
+The tool will output the input file if it is valid.
+
+-----
+
+**Columns**
+
+ * user_specimen_id
+ * field_call
+ * bcoral_genet_id
+ * bsym_genet_id
+ * reef
+ * region
+ * latitude
+ * longitude
+ * geographic_origin
+ * colony_location
+ * depth
+ * disease_resist
+ * bleach_resist
+ * mortality
+ * tle
+ * spawning
+ * collector_last_name
+ * collector_first_name
+ * org
+ * collection_date
+ * contact_email
+ * seq_facility
+ * array_version
+ * public
+ * public_after_date
+ * sperm_motility
+ * healing_time
+ * dna_extraction_method
+ * dna_concentration
+ * registry_id
+ * result_folder_name
+ * plate_barcode
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{None,
+            journal = {None},
+            author = {Baums I},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {http://baumslab.org}
+        </citation>
+    </citations>
+</tool>
+