Mercurial > repos > recetox > matchms_filtering

changeset 1:2f9c19fa4346 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:22:45 +0000
parents 6303b43e29cb
children b8bf66da7e6f
files macros.xml matchms_filtering.xml
diffstat 2 files changed, 76 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jan 28 16:22:45 2022 +0000
@@ -0,0 +1,70 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.11.0</token>
+
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
+    <token name="@HELP_matchms@">
+        <![CDATA[
+            Documentation
+                For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
+                and https://matchms.readthedocs.io/en/latest/.
+
+            Upstream Tools
+                +-----------+---------------+--------+-----------+
+                | Name      | Output File   | Format | Parameter |
+                +===========+===============+========+===========+
+                | RAMClustR | Mass spectra  | msp    | references|
+                +-----------+---------------+--------+-----------+
+                | RAMClustR | Mass spectra  | msp    | queries   |
+                +-----------+---------------+--------+-----------+
+
+            Downstream Tools
+                The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks.
+        ]]>
+    </token>
+
+    <token name="@HELP_formatter@">
+        <![CDATA[
+            Usage
+                This tool creates user friendly tables from the data matrices produces by matchms.
+                The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
+
+            Input Table Format
+                The tool expects two data matrices with the format as depicted below.
+                The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
+
+                +----------+------+------+-----+
+                |          | C001 | C002 | ... |
+                +==========+======+======+=====+
+                | Perylene | 0.1  | 0.0  | ... |
+                +----------+------+------+-----+
+                | Glycine  | 0.5  | 0.34 | ... |
+                +----------+------+------+-----+
+                |   ...    | ...  | ...  | ... |
+                +----------+------+------+-----+
+
+            Output Table Format
+                +----------+-----------+---------+--------+
+                | query    | reference | matches | scores |
+                +==========+===========+=========+========+
+                | C001     | Glycine   |      6  | 0.5    |
+                +----------+-----------+---------+--------+
+                | C002     | Glycine   |     3   | 0.34   |
+                +----------+-----------+---------+--------+
+                |   ...    | ...       | ...     | ...    |
+                +----------+-----------+---------+--------+
+        ]]>
+    </token>
+</macros>
--- a/matchms_filtering.xml	Mon Jan 24 11:15:00 2022 +0000
+++ b/matchms_filtering.xml	Fri Jan 28 16:22:45 2022 +0000
@@ -1,7 +1,11 @@
-<tool id="matchms_filtering" name="matchMS filtering" version="0.11.0+galaxy0">
+<tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy0">
     <description>filter and normalize mass spectrometry data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
     <requirements>
-        <requirement type="package" version="0.11.0">matchms</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
         <requirement type="package" version="1.1.4">pandas</requirement>
     </requirements>