diff merge_flags.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_flags.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,79 @@
+<tool id="secimtools_merge_flags" name="Merge Flag Files" version="@WRAPPER_VERSION@">
+    <description>with the same unique identifiers into a single file.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+merge_flags.py
+--input "$input"
+--output "$output"
+#set names = '" "'.join( [ str( $i.display_name ) for $i in $input ] )
+--filename "${names}"
+#if $flagUniqID
+    --flagUniqID $flagUniqID
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" format="tabular" type="data"  label="Input Flag Files" multiple="true" help="Input your tab-separated flag files. CTRL+CLICK to select multiple files. If not tab separated see TIP below." />
+        <param name="flagUniqID" type="text" size="30" value="" label="Unique identifier in the flag files (feature or sample)" help="Name of the column in your flag file that contains unique identifiers."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}: Flags"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"      value="ST000006_run_order_regression_flags.tsv,ST000006_lasso_enet_var_select_flags.tsv"/>
+            <param name="flagUniqID" value="Retention_Index" />
+            <param name="filename"   value="ST000006_run_order_regression_flags ST000006_lasso_enet_var_select_flags" />
+            <output name="output"    file="ST000006_merge_flags_output.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool merges two or more flag files together.  The flag files can be either in wide format or in design format.
+
+The merging requirements are:
+
+(1) the number of rows should be the same in all files being merged and
+(2) all files should contain the same unique ID column name to merge by.
+
+**Note:** More broadly, the tool can merge non-metabolomics data as long ast he above requirements are met.
+
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two or more datasets are required.
+
+@WIDE@
+
+**NOTE:** The sample IDs must match the sample IDs in the Design File (below).
+Extra columns will automatically be ignored.
+
+@METADATA@
+
+**Unique ID for Flag file (feature ID or sample ID).**
+
+    - Name of the column in your Flag file that contains unique IDs.
+
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The TSV output contains all columns from the flag files.  The column with the unique row ID will be included once in the output dataset.
+
+**Note:** If the input flag files have the same flag column name in multiple files,  the merged file will have columns from all imputed files.
+To distinguish columns obtained from different files, column names will be altered by appending the corresponding file name to the end of the column name.
+All non-supported file name characters will be changed to ‘_’.
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>