Mercurial > repos > iuc > query_tabular

diff query_tabular.xml @ 10:f777a82b7a15 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
author iuc
date Thu, 24 Sep 2020 11:24:32 +0000
parents 4903740da8bc
children b6100c4d40e0
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line diff
--- a/query_tabular.xml	Sat Sep 12 01:20:27 2020 +0000
+++ b/query_tabular.xml	Thu Sep 24 11:24:32 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="query_tabular" name="Query Tabular" version="3.1.0">
+<tool id="query_tabular" name="Query Tabular" version="3.1.1">
     <description>using sqlite sql</description>
 
     <macros>
@@ -528,6 +528,57 @@
             <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
         </test>
 
+        <test>
+            <repeat name="tables">
+                <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
+                <section name="input_opts">
+                    <repeat name="linefilters">
+                        <conditional name="filter">
+                            <param name="filter_type" value="regex"/>
+                            <param name="regex_pattern" value="peptide"/>
+                            <param name="regex_action" value="include_find"/>
+                        </conditional>
+                    </repeat>
+                </section>
+                <section name="tbl_opts">
+                    <param name="table_name" value="epitope"/>
+                    <param name="column_names_from_first_line" value="True"/>
+                </section>
+            </repeat>
+            <param name="sqlquery" value="SELECT * FROM epitope"/>
+            <conditional name="query_result">
+                <param name="header" value="yes"/>
+                <param name="header_prefix" value=""/>
+            </conditional>
+            <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/>
+        </test>
+
+        <test>
+            <repeat name="tables">
+                <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
+                <section name="input_opts">
+                    <repeat name="linefilters">
+                        <conditional name="filter">
+                            <param name="filter_type" value="regex"/>
+                            <param name="regex_pattern" value="NOT TO BE FOUND"/>
+                            <param name="regex_action" value="include_find"/>
+                        </conditional>
+                    </repeat>
+                </section>
+                <section name="tbl_opts">
+                    <param name="table_name" value="epitope"/>
+                    <param name="column_names_from_first_line" value="False"/>
+                    <param name="col_names" value="pos,peptide,logscore,,,,Allele"/>
+                </section>
+            </repeat>
+            <param name="sqlquery" value="SELECT pos,peptide,logscore,Allele FROM epitope"/>
+            <conditional name="query_result">
+                <param name="header" value="yes"/>
+                <param name="header_prefix" value=""/>
+            </conditional>
+            <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/>
+        </test>
+
     </tests>
     <help><![CDATA[
 =============
@@ -540,6 +591,13 @@
 
   An existing SQLite_ data base can be used as input, and any selected tabular datasets will be added as new tables in that data base.
 
+    **NOTE:** If there are no data rows in an input tabular dataset, query_tabular will fail unless:
+
+      - There is a row header line in the dataset and **Use first line as column names** is selected  
+      - **Specify Column Names** is used to provide column names
+
+        in which case an empty table will be created with those columns
+
 
 @LINEFILTERS_HELP@