--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gather.xml	Tue May 19 17:21:15 2020 -0400
@@ -0,0 +1,197 @@
+<tool id="csvtk_gather" name="csvtk-gather" version="@VERSION@+@GALAXY_VERSION@">
+    <description> column(s) into key-value pairs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_cmd" />
+    <command detect_errors="exit_code"><![CDATA[
+
+###################
+## Start Command ##
+###################
+csvtk gather --num-cpus "\${GALAXY_SLOTS:-1}"
+
+    ## Add additional flags as specified ##
+    #######################################
+    $global_param.illegal_rows
+    $global_param.empty_rows
+    $global_param.header
+    $global_param.lazy_quotes
+
+    ## Set Tabular input/output flag if first input is tabular ##
+    #############################################################
+    #if $in_1.is_of_type("tabular"):
+        -t -T
+    #end if
+
+    ## Set input files ##
+    #####################
+    $in_1
+
+    ## Specify fields to use ##
+    ###########################
+    -F -f '$column_text.in_text'
+
+    ## Specific inputs ##
+    #####################
+    -k '$key_string'
+    -v '$value_string'
+    
+    ## Keep only Key/value columns ##
+    #################################
+    #if $only_input_columns == 'Yes'
+        | csvtk cut -F -f '$key_string','$value_string'
+
+        #if $in_1.is_of_type("tabular"):
+            -t -T
+        #end if
+    #end if
+
+    ## To output ##
+    ###############
+    > gathered
+
+    ]]></command>
+    <inputs>
+        <expand macro="singular_input"/>
+        <expand macro="fields_input"/>
+        <param name="key_string" type="text"
+            optional="false"
+            argument="-k"
+            label="Name of Key Column"
+            help="Set name of key column that gathered field will output to">
+            <expand macro="text_sanitizer" />
+        </param>
+        <param name="value_string" type="text"
+            optional="false"
+            argument="-v"
+            label="Name of Value Column">
+            <expand macro="text_sanitizer" />
+        </param>
+        <param name="only_input_columns" type="boolean"
+            truevalue="Yes"
+            falsevalue="No"
+            label="Keep only Key and Value column(s) generated"
+            help="Removes all columns but the input labeled key and value columns"
+        />
+        <expand macro="global_parameters" />
+    </inputs>
+    <outputs>
+        <data format_source="in_1" from_work_dir="gathered" name="gathered" label="${in_1.name} gathered on column(s) ${column_text.in_text}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_1" value="csv.csv" />
+            <param name="key_string" value="1" />
+            <param name="value_string" value="2" />
+            <conditional name="column_text">
+                <param name="select" value="string" />
+                <param name="in_text" value="1" />
+            </conditional>
+            <output name="gathered" file="gathered.csv" ftype="csv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    
+Csvtk - Gather Help
+-------------------
+
+Info
+####
+
+Csvtk gather gathers columns into key-value pairs
+
+.. class:: warningmark
+
+    Single quotes are not allowed in text inputs!
+
+@HELP_INPUT_DATA@
+
+
+Usage
+#####
+
+**Ex. Gather with column 1:**
+
+Suppose we had the following table:
+
++---------+------------+-----------+
+| Name    | Blood Type | Frequency |
++=========+============+===========+
+| Bob     | A          | 4         |
++---------+------------+-----------+
+| Jacob   | B          | 5         |
++---------+------------+-----------+
+| Matthew | O          | 12        |
++---------+------------+-----------+
+| Daniel  | AB         | 1         |
++---------+------------+-----------+
+
+If we did a gather on column 1 creating a key column called "Key" and a value column called "Output"
+we would get the following result.
+
++------------+-----------+------+---------+
+| Blood Type | Frequency | Key  | Output  |
++============+===========+======+=========+
+| A          | 4         | Name | Bob     |
++------------+-----------+------+---------+
+| B          | 4         | Name | Jacob   |
++------------+-----------+------+---------+
+| O          | 12        | Name | Matthew |
++------------+-----------+------+---------+
+| AB         | 1         | Name | Daniel  |
++------------+-----------+------+---------+
+
+----
+
+**Ex. Gather with 2 columns:**
+
+Same starting table
+
++---------+------------+-----------+
+| Name    | Blood Type | Frequency |
++=========+============+===========+
+| Bob     | A          | 4         |
++---------+------------+-----------+
+| Jacob   | B          | 5         |
++---------+------------+-----------+
+| Matthew | O          | 12        |
++---------+------------+-----------+
+| Daniel  | AB         | 1         |
++---------+------------+-----------+
+
+Now, if we specify the input columns as "1,2" to get columns 1 and 2 targeted as the key columns (called key),
+we get the following output:
+
++-----------+------------+---------+
+| Frequency | Key        | Output  |
++===========+============+=========+
+| 4         | Name       | Bob     |
++-----------+------------+---------+
+| 4         | Blood Type | A       |
++-----------+------------+---------+
+| 4         | Name       | Jacob   |
++-----------+------------+---------+
+| 4         | Blood Type | B       |
++-----------+------------+---------+
+| 12        | Name       | Matthew |
++-----------+------------+---------+
+| 12        | Blood Type | O       |
++-----------+------------+---------+
+| 1         | Name       | Daniel  |
++-----------+------------+---------+
+| 1         | Blood Type | AB      |
++-----------+------------+---------+
+
+----
+
+@HELP_COLUMNS@
+
+
+@HELP_END_STATEMENT@
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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