--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hdf5_to_txt.xml	Sat Apr 11 16:45:45 2020 -0400
@@ -0,0 +1,174 @@
+<tool id="dimspy_hdf5_to_txt" name="Convert DIMSpy-based HDF5 to tsv" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        #if $input.object_type == 'peak_lists'
+            dimspy hdf5-pls-to-txt
+            --input '$input.hdf5_file_in'
+            --output .
+            --delimiter $delimiter
+        #elif $input.object_type == 'peak_matrix'
+            #if $input.matrix_format == 'standard' or $input.matrix_format == 'standard_comprehensive'
+                dimspy hdf5-pm-to-txt
+                --input '$input.hdf5_file_in'
+                --output '$matrix_file_out'
+                --delimiter $delimiter
+                --attribute_name $input.matrix_attr
+                --representation-samples $input.representation_samples
+            #end if
+            #if $input.matrix_format == "standard_comprehensive"
+                &&
+            #end if
+            #if $input.matrix_format == 'comprehensive' or $input.matrix_format == 'standard_comprehensive'
+                dimspy hdf5-pm-to-txt
+                --input '$input.hdf5_file_in'
+                --output '$matrix_comprehensive_file_out'
+                --delimiter $delimiter
+                --comprehensive
+                --attribute_name '$input.matrix_attr'
+                --representation-samples $input.representation_samples
+            #end if
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
+        <conditional name="input">
+            <param name="object_type" type="select" label="Content HDF5 file" help="">
+                <option value="peak_matrix" selected="true">Peak Intensity Matrix</option>
+                <option value="peak_lists">Peak list(s)</option>
+            </param>
+            <when value="peak_lists">
+                <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklist(s) (HDF5 file)" help="" />
+            </when>
+            <when value="peak_matrix">
+                <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak intensity matrix (HDF5 file)" help="" />
+                <param name="matrix_format" type="select" label="Select format(s) tsv formatted peak instensity matrix" help="">
+                    <option value="standard" selected="true">Standard Peak Matrix (i.e. m/z and intensity).</option>
+                    <option value="comprehensive">Comprehensive Peak Matrix (e.g. m/z and intensity, rsd, missing values).</option>
+                    <option value="standard_comprehensive">Standard and comprehensive</option>
+                </param>
+                <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">
+                    <option value="rows" selected="true">Rows</option>
+                    <option value="columns">Columns</option>
+                </param>
+                <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">
+                    <option value="intensity" selected="true">Intensity</option>
+                    <option value="mz">m/z</option>
+                    <option value="snr">Signal-to-noise ratio (SNR)</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
+            <filter>input["object_type"] == "peak_lists"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
+        </collection>
+        <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix">
+            <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "standard" or input["matrix_format"] == "standard_comprehensive")</filter>
+        </data>
+        <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix (comprehensive)" >
+            <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "comprehensive" or input["matrix_format"] == "standard_comprehensive")</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="input">
+                <param name="object_type" value="peak_lists"/>
+                <param name="hdf5_file_in" value="pls.h5" ftype="h5"/>
+            </conditional>
+            <output_collection name="peaklists_txt" type="list">
+                <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262.txt" ftype="tsv"/>
+                <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263.txt" ftype="tsv"/>
+                <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264.txt" ftype="tsv"/>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="input">
+                <param name="object_type" value="peak_matrix"/>
+                <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
+                <param name="matrix_format" value="comprehensive"/>
+                <param name="representation_samples" value="columns"/>
+                <param name="matrix_attr" value="intensity"/>
+            </conditional>
+            <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_intensity.txt" ftype="tsv"/>
+        </test>
+        <test>
+            <conditional name="input">
+                <param name="object_type" value="peak_matrix"/>
+                <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
+                <param name="matrix_format" value="standard"/>
+                <param name="representation_samples" value="rows"/>
+                <param name="matrix_attr" value="mz"/>
+            </conditional>
+            <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_mz.txt" ftype="tsv"/>
+        </test>
+        <test>
+            <conditional name="input">
+                <param name="object_type" value="peak_matrix"/>
+                <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
+                <param name="matrix_format" value="standard_comprehensive"/>
+                <param name="representation_samples" value="rows"/>
+                <param name="matrix_attr" value="snr"/>
+            </conditional>
+            <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_snr.txt" ftype="tsv"/>
+            <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_comprehensive_snr.txt" ftype="tsv"/>
+        </test>
+    </tests>
+    <help>
+--------------------------------
+Convert DIMSpy-based HDF5 to tsv
+--------------------------------
+
+..
+
+----------------------------------
+
+Description
+-----------
+
+This tool converts a .hdf5 file, containing either peaklist(s) or a peak intensity matrix, to user-friendly .tsv file(s).
+
+----------------------------------
+
+Parameters
+----------
+
+**Contents of hdf5 file** (REQUIRED; default = **peak intensity matrix**) - selection menu in which the user defines whether the input .hdf5 file contains:
+
+- **a peak intensity matrix**
+
+- **peaklist(s)**
+
+|
+
+**Peak intensity matrix or peaklists (HDF5 file)** (REQUIRED) - selection menu in which the user chooses the .hdf5 file (from the active Galaxy history) to be converted to .tsv formatted output(s). 
+
+|
+
+**Select format(s) tsv formatted peak intensity matrix** (REQUIRED; default = **Standard Peak Matrix**) - selection menu in which the user chooses from the following export options:
+ 
+@help_options_addtional_output@
+
+----------------------------------
+
+Output file(s)
+--------------
+
+**Important** - the metric recorded output peak matrix/matrices is adjusted using the "The peak matrix should contain intensity | m/z | SNR values" parameter. By default, samples are presented row-wise and peak mass-to-charge ratio values are presented column-wise in each peak matrix, though this may be adjusted using the "Should rows or columns represent samples" parameter toggle. 
+
+@help_outputs_matrix@
+
+----------------------------------------------
+
+@github_developers_contributors@
+@license@
+    </help>
+    <expand macro="citations" />
+</tool>
+