--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_samples.xml	Sat Apr 11 16:51:19 2020 -0400
@@ -0,0 +1,140 @@
+<tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description> - Align peaks across Peaklists</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        dimspy align-samples
+        --input '$hdf5_file_in'
+        --output '$hdf5_file_out'
+        #if $filelist
+            --filelist '$filelist'
+        #end if
+        --ppm $ppm
+        #if $hdf5_to_txt.standard
+            &&
+            @HDF5_PM_TO_TXT@
+        #end if
+        #if $hdf5_to_txt.comprehensive
+            &&
+            @HDF5_PM_TO_TXT_COMPREHENSIVE@
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" />
+        <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for  Process Scans or Replicate Filter." />
+        <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
+        <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
+        <expand macro="hdf5_pm_to_txt" />
+    </inputs>
+    <outputs>
+        <expand macro="outputs_peak_intensity_matrix" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
+            <param name="ppm" value="2.0"/>
+            <param name="delimiter" value="tab"/>
+            <conditional name="hdf5_to_txt" >
+                <param name="standard" value="True"/>
+                <param name="comprehensive" value="False"/>
+                <param name="samples_representations" value="rows"/>
+                <param name="matrix_attr" value="intensity"/>
+            </conditional>
+            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
+            <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
+        </test>
+        <test>
+            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
+            <param name="ppm" value="2.0"/>
+            <param name="delimiter" value="tab"/>
+            <conditional name="hdf5_to_txt">
+                <param name="standard" value="True"/>
+                <param name="comprehensive" value="False"/>
+                <param name="representation_samples" value="columns"/>
+                <param name="matrix_attr" value="intensity"/>
+            </conditional>
+            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
+            <output name="matrix_file_out" file="peak_matrix_as_t.txt" ftype="tsv"/>
+        </test>
+        <test>
+            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
+            <param name="ppm" value="2.0"/>
+            <param name="delimiter" value="tab"/>
+            <conditional name="hdf5_to_txt">
+                <param name="standard" value="True"/>
+                <param name="comprehensive" value="True"/>
+                <param name="samples_representations" value="rows"/>
+                <param name="matrix_attr" value="mz"/>
+            </conditional>
+            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
+            <output name="matrix_file_out" file="peak_matrix_as_mz.txt" ftype="tsv"/>
+            <output name="matrix_comprehensive_file_out" file="peak_matrix_as_mz_compr.txt" ftype="tsv"/>
+        </test>
+    </tests>
+    <help>
+-------------
+Align Samples
+-------------
+
+..
+
+-------------------------------
+
+Description
+-----------
+
+Standard DIMS processing workflow: Process Scans -> Replicate Filter -> **Align Samples** -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
+
+|
+
+This tool takes the peaklists for all study samples and merges them in to single aligned peak matrix. The peak matrix comprises a table, with samples along one axis and the mass-to-charge ratios of detected mass spectral peaks along the opposite axis. At the intersection of sample and mass-to-charge ratio, the intensity is given for a specific peak in a specific sample (if no intensity recorded, then ‘0’ is inserted).
+
+-------------------------------
+
+Parameters
+----------
+
+**Peaklists (HDF5 file)** (REQUIRED) - a HDF5 file containing all peaklists to undergo alignment.
+
+|
+
+**Filelist / Samplelist** (REQUIRED) - a file of type ‘tabular’ with the following required columns (additional metadata columns may also be included, e.g. “collectionTime”, etc.):
+
+    - **filename** - the name of the .raw or .mzML files from which peaklists were extracted using the “Process Scans” tool
+    
+    - **batch** - a numeric value indicating the analysis batches samples were analysed in (if a single large analytica run then the default = 1)
+
+    - **classLabel** - a string indicating the experiment classes the samples belong to (e.g. control, QC, blank/placebo, exposed/treatment)
+
+    - **injectionOrder** - a numeric value indicating the order in which samples were analysed.
+
+|
+
+**ppm error tolerance** (REQUIRED; default = 2.0) - a numeric value equal-to or greater-than 0. 
+
+This parameter will influence the alignment of peaks from input peaklists. Peaks from distinct peaklists (corresponding to individual study samples) are aligned if the difference between their mass-to-charge ratios, when divided by the average of their mass-to-charge ratios and multiplied by 1 × 10\ :sup:`6` \, is equal-to or less-than than this parameter value (i.e. the difference between the mass-to-charge ratios, measured on the ppm scale, is less than the user-defined “ppm error tolerance”). 
+
+|
+
+@help_options_addtional_output@
+
+|
+
+------------------------------
+
+Output file(s)
+--------------
+
+@help_outputs_matrix@
+
+-------------------------------------------------------------
+
+@github_developers_contributors@
+@license@
+    </help>
+    <expand macro="citations" />
+</tool>