--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collapse.xml	Tue May 19 17:18:56 2020 -0400
@@ -0,0 +1,193 @@
+<tool id="csvtk_collapse" name="csvtk-collapse" version="@VERSION@+@GALAXY_VERSION@">
+    <description> one field with selected fields as keys</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_cmd" />
+    <command detect_errors="exit_code"><![CDATA[
+
+###################
+## Start Command ##
+###################
+
+csvtk collapse --num-cpus "\${GALAXY_SLOTS:-1}"
+
+    ## Add additional flags as specified ##
+    #######################################
+    $ignore_case
+    $global_param.illegal_rows
+    $global_param.empty_rows
+    $global_param.header
+    $global_param.lazy_quotes
+
+    ## Set Tabular input/output flag if input is tabular ##
+    #######################################################
+    #if $in_1.is_of_type("tabular"):
+        -t -T
+    #end if
+
+    ## Set Input ##
+    ###############
+    '$in_1'
+
+    ## Specify fields for collapse ##
+    #################################
+    -F -f '$column_text.in_text'
+
+    ## other ##
+    ###########
+    -v '$value_column.in_text'
+    -s '$separator'
+
+    ## To output ##
+    ###############
+    > collapsed
+
+    ]]></command>
+    <inputs>
+        <expand macro="singular_input" />
+        <expand macro="fields_input" />
+        <conditional name="value_column" >
+            <param type="select" name="select" label="Select value column to collapse based on" argument="-v">
+                <option value="string">Column Name</option>
+                <option value="column">Column Number</option>
+            </param>
+            <when value="column">
+                <param type="data_column" name="in_text"
+                    data_ref="in_1"
+                    multiple="false"
+                    label="Input column number"
+                    help="Select column to collapse on"
+                />
+            </when>
+            <when value="string">
+                <param type="text" name="in_text"
+                    optional="false"
+                    label="Input column name"
+                    help="Specify column name or number (ex. 1 for first column) to collapse on">
+                    <expand macro="text_sanitizer" />
+                </param>
+            </when>
+        </conditional>
+        <param name="separator" type="text" value="; " argument="-s"
+            optional="false"
+            label="Separator string"
+            help="Input string of characters that will separate collapsed columns. The ' character is not allowed">
+            <expand macro="text_sanitizer" />
+        </param>
+        <expand macro="ignore_case" />
+        <expand macro="global_parameters" />
+    </inputs>
+    <outputs>
+        <data format_source="in_1" name="collapse" from_work_dir="collapsed" label="${in_1.name} with ${value_column.in_text} collapsed by ${column_text.in_text}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_1" value="blood_type.tsv" />
+            <conditional name="column_text">
+                <param name="select" value="string" />
+                <param name="in_text" value="2" />
+            </conditional>
+            <conditional name="value_column">
+                <param name="select" value="string" />
+                <param name="in_text" value="1" />
+            </conditional>
+            <param name="separator" value="; " />
+            <output name="collapse" file="collapsed.tsv" ftype="tabular" />
+        </test>
+        <test>
+        <param name="in_1" value="illegal.csv" />
+            <conditional name="column_text">
+                <param name="select" value="string" />
+                <param name="in_text" value="4" />
+            </conditional>
+            <conditional name="value_column">
+                <param name="select" value="string" />
+                <param name="in_text" value="1" />
+            </conditional>
+            <param name="separator" value="; " />
+            <section name="global_param">
+                <param name="illegal_rows" value="true" />
+            </section>
+            <output name="collapse" file="illegal_collapse.csv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    
+Csvtk - Collapse Help
+---------------------
+
+Info
+####
+
+Csvtk collapse combines one field with selected fields as keys for what to combine
+
+.. class:: warningmark
+
+    Single quotes are not allowed in text inputs!
+
+@HELP_INPUT_DATA@
+
+
+Usage
+#####
+
+To run csvtk-collapse, all you need is a valid (as defined above) CSV or TSV file with a column you want to use
+to collapse on based on any number of key column(s).
+
+**Example collapse with one key column**
+
+Input table:
+
++--------+--------+----------+
+| Name   | Colour | Food     |
++========+========+==========+
+| Eric   | Blue   | Apples   |
++--------+--------+----------+
+| Darian | Blue   | Pancakes |
++--------+--------+----------+
+| Daniel | Red    | Apples   |
++--------+--------+----------+
+| Emily  | Blue   | Apples   |
++--------+--------+----------+
+
+Now if you wanted to find out who has the same favourite colour, you would specify the key column as "Colour" (-F -f)
+and the value column as "Name" (-v) to generate the following table:
+
++--------+---------------------+
+| Colour | Name                |
++========+=====================+
+| Red    | Daniel              |
++--------+---------------------+
+| Blue   | Eric; Darian; Emily |
++--------+---------------------+
+
+--------
+
+**Example collapse with two key columns**
+
+Same input table, now our key columns are "Colour" and "Food" which could be input as "2,3" (-F -f)
+and the same value column which would generate the following table:
+
++--------+----------+-------------+
+| Colour | Food     | Name        |
++========+==========+=============+
+| Blue   | Pancakes | Darian      |
++--------+----------+-------------+
+| Red    | Apples   | Daniel      |
++--------+----------+-------------+
+| Blue   | Apples   | Eric; Emily |
++--------+----------+-------------+
+
+----
+
+@HELP_COLUMNS@
+
+
+@HELP_END_STATEMENT@
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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