Mercurial > repos > rv43 > test_tomo_reconstruct

diff tomo_reconstruct.xml @ 0:98e23dff1de2 draft default tip

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 16:22:42 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_reconstruct.xml	Tue Mar 21 16:22:42 2023 +0000
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+<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" python_template_version="3.9">
+    <description>Perform a tomography reconstruction</description>
+    <macros>
+        <import>tomo_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+            mkdir tomo_reconstruct_plots;
+            $__tool_directory__/tomo_reconstruct.py
+            --input_file "$input_file"
+            --center_file "$center_file"
+            --output_file "output.nex"
+            --galaxy_flag
+            -l "$log"
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="common_inputs"/>
+        <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
+        <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
+    </inputs>
+    <outputs>
+        <expand macro="common_outputs"/>
+        <collection name="tomo_reconstruct_plots" type="list" label="Data recontructed images">
+            <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
+        </collection>
+        <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
+    </outputs>
+    <help><![CDATA[
+        Reconstruct tomography images.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>