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planemo upload commit ea1ea6d651e2198be296c8f71270b693c762396c
author workflow4metabolomics
date Tue, 22 Nov 2022 15:12:06 +0000
parents
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files physiofit_manager.xml test-data/biomass.tsv test-data/concentrations.tsv test-data/output.tsv
diffstat 4 files changed, 68 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/physiofit_manager.xml	Tue Nov 22 15:12:06 2022 +0000
@@ -0,0 +1,48 @@
+<tool id='physiofit_data_manager' name='PhysioFit Manager' profile='21.09' version='@TOOL_VERSION@+galaxy0'>
+    <description>Managing inputs for PhysioFit</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.1</token>
+    </macros>
+    <requirements>
+        <requirement type='package' version='@TOOL_VERSION@'>physiofit_data_manager</requirement>
+    </requirements>
+    <command detect_errors='exit_code'><![CDATA[
+
+        physiofit_manager
+        -b '$biomass_file'
+        -c '$concentrations_file'
+        -e '$physiofit_input'
+
+    ]]></command>
+    <inputs>
+        <param name='biomass_file' type='data' format='tabular,txt' multiple='true' label='File containing the time-course measurements of biomass concentrations' />
+        <param name='concentrations_file' type='data' format='tabular,txt' multiple='true' label='File containing the time-course measurements of the different metabolite concentrations' />
+    </inputs>
+
+    <outputs>
+        <data name='physiofit_input' format='tabular' label='PhysioFit Input File' />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name='biomass_file' value='biomass.tsv' />
+            <param name='concentrations_file' value='concentrations.tsv' />
+            <output name='physiofit_input' value='output.tsv' />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+.. class:: warningmark
+
+Tool to handle physiofit input files
+
+    ]]></help>
+    <citations>
+        <citation type='bibtex'>
+    @misc{githubphysiofit,
+      author = {Le Gregam, Loic},
+      year = {2022},
+      title = {PhysioFit_Data_Manager},
+    }</citation>
+        </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biomass.tsv	Tue Nov 22 15:12:06 2022 +0000
@@ -0,0 +1,6 @@
+time	X
+1	0.5
+2	0.8
+3	1.2
+4	1.8
+5	1.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/concentrations.tsv	Tue Nov 22 15:12:06 2022 +0000
@@ -0,0 +1,6 @@
+time	glc
+1	8
+1.5	7
+3	5
+4.20	3
+5	1
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tsv	Tue Nov 22 15:12:06 2022 +0000
@@ -0,0 +1,8 @@
+time	X	glc
+1.0	0.5	8.0
+1.5	nan	7.0
+2.0	0.8	nan
+3.0	1.2	5.0
+4.0	1.8	nan
+4.2	nan	3.0
+5.0	1.9	1.0