v2.0.0+galaxy0 (#11)

* Bump dimspy version to v2.0.0 (first release py3) * Fix and update tests * Minor Improvements help sections * Update README.rst Co-authored-by: Tomnl <[email protected]>
computational-metabolomics · Apr 28, 2020 · 680116d · 680116d
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
-tool_test_output.*
+tools/dimspy/tool_test_output.*
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/README.rst b/README.rst
@@ -1,6 +1,6 @@
 Galaxy tool wrappers for DIMSpy
-========================
-|Build Status (Travis)| |Git| |Bioconda| |License|
+===============================
+|Build Status (Travis)| |galaxy-eu| |Git| |Bioconda| |License|
 
 Galaxy tool wrappers for Python package DIMSpy: data processing of direct-infusion mass spectrometry (DIMS)-based metabolomics and lipidomics data
 
@@ -11,19 +11,27 @@ PyPI (The Python Package Index): https://pypi.org/project/dimspy
 
 Version
 --------
-v1.4.0+Galaxy0 (`DIMSpy v1.4.0 <https://pypi.org/project/dimspy/1.4.0/>`_)
+v2.0.0+Galaxy0 (`DIMSpy v2.0.0 <https://pypi.org/project/dimspy/2.0.0/>`_)
 
 
 Galaxy
 -------
 `Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. 
 
 
-Authors, contributors & Contacts
-----------------------------------
- - Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
- - Thomas N. Lawson ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
- - Martin R. Jones ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
+Credits
+-------
+
+**Authors and contributors**
+ - Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/staff/profiles/biosciences/weber-ralf.aspx>`__
+ - Thomas N. Lawson ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`__
+ - Martin R. Jones ([email protected]) - `Eawag  (Switzerland) <https://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/martin-jones/show/>`_
+
+
+**DIMSpy acknowledges support from the following funders:**
+ - BBSRC, grant number BB/M019985/1
+ - European Commission's H2020 programme, grant agreement number 654241
+ - Wellcome Trust, grant number 202952/Z/16/Z
 
 
 Bugs
@@ -36,8 +44,10 @@ will help you to make the PR if you are new to `git`.
 
 Changes
 -------
+v2.0.0+galaxy0
+  - First release (Python 3-based version `DIMSpy <https://pypi.org/project/dimspy/2.0.0/>`_)
+
 v1.4.0+galaxy0
-  - First stable release
   - Final release (Python 2-based version `DIMSpy <https://pypi.org/project/dimspy/1.4.0/>`_)
 
 
@@ -59,6 +69,9 @@ section 3.3 of the RawFileReader License, and is not granted rights to redistrib
 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
    :target: https://github.com/computational-metabolomics/dimspy
 
+.. |galaxy-eu| image:: https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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
+   :target: http://usegalaxy.eu
+
 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
    :target: http://bioconda.github.io/recipes/dimspy/README.html
 

diff --git a/tools/dimspy/align_samples.xml b/tools/dimspy/align_samples.xml
@@ -87,7 +87,7 @@ Align Samples
 Description
 -----------
 
-Standard DIMS processing workflow: Process Scans -> Replicate Filter -> **Align Samples** -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
+Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> **Align Samples** -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
 
 |
 

diff --git a/tools/dimspy/blank_filter.xml b/tools/dimspy/blank_filter.xml
@@ -104,7 +104,7 @@ Blank Filter
 Description
 -----------
 
-Standard DIMS processing workflow: Process Scans -> Replicate Filter -> Align Samples -> [Missing values sample filter] -> **Blank Filter** -> Sample Filter -> Matrix processing -> Statistics
+Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> Align Samples -> **Blank Filter** -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
 
 |
 

diff --git a/tools/dimspy/macros.xml b/tools/dimspy/macros.xml
@@ -1,12 +1,13 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.4.0</token>
+    <token name="@TOOL_VERSION@">2.0.0</token>
     <token name="@GALAXY_TOOL_VERSION@">0</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">dimspy</requirement>
         </requirements>
     </xml>
+
 
     <token name="@HDF5_PM_TO_TXT@">
         dimspy hdf5-pm-to-txt

diff --git a/tools/dimspy/merge_peaklists.xml b/tools/dimspy/merge_peaklists.xml
@@ -10,52 +10,60 @@
         #for $fn in $hdf5_files_in
             --input '$fn'
         #end for
-        #if $multilist.flag == 'true'
+
+        #if $multilist
             --output .
-            --filelist $multilist.filelist'
         #else
             --output '$hdf5_file_out'
-            #if $filelist
-                --filelist '$multilist.filelist'
-            #end if
+        #end if
+
+        #if $filelist
+           --filelist '$filelist'
         #end if
     ]]>
     </command>
     <inputs>
-        <param name="hdf5_files_in" argument="--input" type="data" format="h5" multiple="true" min="2" label="Peaklist to merge" help="Select a minimum of two hdf5 files" />
-        <conditional name="multilist">
-            <param name="flag" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Create multiple merged peaklists?" help="Based on a 'multilist' column in the filelist text file, divide the peaklists into different lists
-                                                       e.g. [pl1, pl2, pl3, pl4] can be converted to 2 new lists:
+        <param name="hdf5_files_in" type="data" multiple="true" format="h5" min="2" label="Peaklist to merge" help="Select a minimum of two hdf5 files" argument="--input" />
+        <param name="multilist" type="boolean" checked="false" label="Create multiple merged peaklists?"
+               help="Based on a 'multilist' column in the filelist text file, divide the peaklists into different lists
+                                                       e.g. [pl1 pl2], [pl3, pl4] can be converted to 2 new lists:
                                                             [pl1, pl3] [pl2, pl4]"/>
-            <when value="true">
-                <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" label="Filelist" />
-            </when>
-            <when value="false">
-                <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist" />
-            </when>
-        </conditional>
+        <param type="data" format="tsv,tabular" optional="true" label="Filelist"
+               help="A table containing metadata for each experimental sample. See help section below for more details." argument="--filelist"  />
     </inputs>
     <outputs>
         <collection name="multiple_merged" type="list" label="${tool.name} on ${on_string}: Peaklists (HDF5)">
-            <filter>multilist["flag"] is True</filter>
+            <filter>multilist</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.hdf5" format="h5" directory="." visible="false" />
         </collection>
         <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)">
-            <filter>multilist["flag"] is False</filter>
+            <filter>multilist is False</filter>
         </data>
     </outputs>
     <tests>
         <test>
+            <!-- Merge (no filelist)          -->
             <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" />
             <output name="hdf5_file_out" value="merged_01.h5" ftype="h5" compare="sim_size" />
         </test>
         <test>
+            <!-- Merge (with filelist)        -->
             <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" />
-            <conditional name="multilist">
-                <param name="filelist" value="filelist_merge.txt" ftype="tsv"/>
-            </conditional>
+            <param name="filelist" value="filelist_merge.txt" ftype="tsv"/>
             <output name="hdf5_file_out" value="merged_02.h5" ftype="h5" compare="sim_size" />
         </test>
+        <test>
+            <!-- Merge (multilist)            -->
+            <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" />
+            <param name="filelist" value="filelist_multilist_merge.txt" ftype="tsv"/>
+            <param name="multilist" value="true"/>
+            <output_collection name="multiple_merged" type="list">
+                <element name="merged_peaklist_001" file="merged_peaklist_001.h5" ftype="h5" compare="sim_size" />
+                <element name="merged_peaklist_002" file="merged_peaklist_002.h5" ftype="h5" compare="sim_size" />
+                <element name="merged_peaklist_003" file="merged_peaklist_003.h5" ftype="h5" compare="sim_size" />
+            </output_collection>
+        </test>
+
     </tests>
     <help>
 ---------------
@@ -77,51 +85,59 @@ This tool allows users to extract and export specific peaklists from one or more
 Parameters
 ----------
 
+|
+
 **Peaklist to merge** (REQUIRED; minimally requires two .hdf5 files) - selection menu from which the user must select two or more .hdf5 files from the active Galaxy history.
 
-**NOTE**: if a .hdf5 file containing a peak intensity matrix is selected, then the peaklists used in generating that matrix are extracted from the file e.g. [pl1, pl2, pl3] + [pm456] = [pl1, pl2, pl3] + [pl4, pl5, pl6] = [pl1, pl2, pl3, pl4, pl5, pl6] .
+    **NOTE**: if a .hdf5 file containing a peak intensity matrix is selected, then the peaklists used in generating that matrix are extracted from the file e.g. [pl1, pl2, pl3] + [pm456] = [pl1, pl2, pl3] + [pl4, pl5, pl6] = [pl1, pl2, pl3, pl4, pl5, pl6] .
 
 |
 
 **Create multiple merged peaklists** (REQUIRED; default = “No”) - binary toggle:
 
-    - **No** - all extracted peaklists are exported to a single .hdf5 file in the active Galaxy history. Metadata associated with each peaklist is also captured in this file.
+    **No** - all extracted peaklists are exported to a single .hdf5 file in the active Galaxy history. Metadata associated with each peaklist is also captured in this file.
 
-    - **Yes** - multiple .hdf5 files are exported to the active Galaxy history, each of which containing a user-defined subset of the extracted peaklist(s) in accordance with the “multilist” column of the input “Filelist”, e.g. using the mock filelist shown below, two .hdf5 files would be exported to history:
-
-      The first .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank1_rep1.raw and blank1_rep2.raw], i.e. all filenames associated with multilist value '1'
+    **Yes** - multiple .hdf5 files are exported to the active Galaxy history, each of which containing a user-defined subset of the extracted peaklist(s) in accordance with the “multilist” column of the input “Filelist”, e.g. using the mock filelist shown below, two .hdf5 files would be exported to history:
 
-      The second .hdf5 file would contain peaklists from [blank_rep1.raw, blank_rep2.raw, blank_rep3.raw and blank_rep4.raw], i.e. all filenames associated with multilist value '2'
+    * The first .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank1_rep1.raw and blank1_rep2.raw], i.e. all filenames associated with multilist value '1'
+
+    * The second .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank_rep3.raw and blank_rep4.raw], i.e. all filenames associated with multilist value '2'
+
+    |
+
+
+    **NOTE** - if for each analysed study sample a corresponding blank sample has been analysed, then the multilist column can be used to pair these together in an output .hdf5 file. This enables sample-specific blank filtering at a later stage.
 
-      **NOTE** - if for each analysed study sample a corresponding blank sample has been analysed, then the multilist column can be used to pair these together in an output .hdf5 file. This enables sample-specific blank filtering at a later stage.
 
 |
 
 **Filelist / Samplelist** (OPTIONAL) - a selection menu from which one or more filelists can be selected.
 
-**Mock example of a filelist** - the optional multilist column determines which peaklists are exported together in .hdf5 format. 
-
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| filename        | classLabel | replicate | batch | injectionOrder | multilist | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| sample_rep1.raw | sample     | 1         | 1     | 1              | 1         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| sample_rep2.raw | sample     | 2         | 1     | 2              | 1         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| sample_rep3.raw | sample     | 3         | 1     | 3              | 2         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| sample_rep4.raw | sample     | 4         | 1     | 4              | 2         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| blank_rep1.raw  | blank      | 1         | 1     | 5              | 1         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| blank_rep2.raw  | blank      | 2         | 1     | 6              | 1         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| blank_rep3.raw  | blank      | 3         | 1     | 7              | 2         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| blank_rep4.raw  | blank      | 4         | 1     | 8              | 2         | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
-| ...             | ...        | ...       | ...   | ...            | ...       | [...] |
-+-----------------+------------+-----------+-------+----------------+-----------+-------+
+    **Mock example of a filelist** - the optional multilist column determines which peaklists are exported together in .hdf5 format. 
+
+    |
+
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | filename        | classLabel | replicate | batch | injectionOrder | multilist | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | sample_rep1.raw | sample     | 1         | 1     | 1              | 1         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | sample_rep2.raw | sample     | 2         | 1     | 2              | 1         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | sample_rep3.raw | sample     | 3         | 1     | 3              | 2         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | sample_rep4.raw | sample     | 4         | 1     | 4              | 2         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | blank_rep1.raw  | blank      | 1         | 1     | 5              | 1         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | blank_rep2.raw  | blank      | 2         | 1     | 6              | 1         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | blank_rep3.raw  | blank      | 3         | 1     | 7              | 2         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | blank_rep4.raw  | blank      | 4         | 1     | 8              | 2         | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
+    | ...             | ...        | ...       | ...   | ...            | ...       | [...] |
+    +-----------------+------------+-----------+-------+----------------+-----------+-------+
 
 | 
 
@@ -130,12 +146,16 @@ Parameters
 Output file(s)
 --------------
 
+|
+
 One or more .hdf5 file(s), each containing one or more peaklists.
 
+|
+
 -----------------------------------
 
 @github_developers_contributors@
-@license@
+ 
     </help>
     <expand macro="citations" />
-</tool>
+</tool>
diff --git a/tools/dimspy/missing_values_sample_filter.xml b/tools/dimspy/missing_values_sample_filter.xml
@@ -63,7 +63,7 @@ Missing Values Sample Filter
 Description
 -----------
 
-Standard DIMS processing workflow: Process Scans -> Replicate Filter -> Align Samples -> **[Missing values sample filter]** -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
+Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> Align Samples -> Blank Filter -> Sample Filter -> **[Missing values sample filter]** -> Pre-processing -> Statistics
 
 |
-Original file line number
+Diff line change
@@ Expand Up / @@ -87,7 +87,7 @@ Align Samples @@
     Description
     -----------
-    Standard DIMS processing workflow: Process Scans -> Replicate Filter -> **Align Samples** -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
+    Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> **Align Samples** -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
     |
@@ Expand Down @@