diff spring_model_all.xml @ 0:64cb5fab9c60 draft

"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_model_all.xml	Tue Mar 23 13:57:37 2021 +0000
@@ -0,0 +1,77 @@
+<tool id="spring_model_all" name="SPRING Model-All" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>complex structures</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    spring_model_all.py
+        -p '$pairs'
+        @hhr_source@
+        @pdb_source@
+        -c '$crossreference'
+        -o 'models'
+        -g '$log'
+    ]]>    </command>
+    <inputs>
+        <param name="pairs" type="data" format="tabular" label="Interacting Pairs" help="Tabular 2-column file containing putative protein interaction pairs." />
+        <param name="crossreference" type="data" format="tabular" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
+        <expand macro="hhr_source" />
+        <expand macro="pdb_source" />
+        <expand macro="logfile" />
+    </inputs>
+    <outputs>
+        <collection name="models" type="list" label="SPRING Model Structures">
+            <discover_datasets pattern="__name_and_ext__" directory="models" />
+        </collection>
+        <data format="tabular" name="log" label="SPRING Model Log">
+            <filter>logfile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="pairs" value="model/pairs.txt" ftype="tabular" />
+            <conditional name="hhr_source">
+                <param name="hhr_source_selector" value="history" />
+                <param name="ffindex" value="model/hhr.ffindex" />
+                <param name="ffdata" value="model/hhr.ffdata" />
+            </conditional>
+            <conditional name="pdb_source">
+                <param name="pdb_source_selector" value="history" />
+                <param name="ffindex" value="model/pdb_structures.ffindex" />
+                <param name="ffdata" value="model/pdb_structures.ffdata" />
+            </conditional>
+            <param name="crossreference" value="model/crossreference.txt" />
+            <param name="logfile" value="true" />
+            <output name="log" file="model/log.txt" />
+            <output_collection name="models" type="list" count="1">
+                <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
+            </output_collection>
+        </test>
+        <test>
+            <param name="pairs" value="model/pairs.txt" ftype="tabular" />
+            <conditional name="hhr_source">
+                <param name="hhr_source_selector" value="indexed" />
+                <param name="hhr" value="hhr_model" />
+            </conditional>
+            <conditional name="pdb_source">
+                <param name="pdb_source_selector" value="indexed" />
+                <param name="pdb" value="pdb01_model" />
+            </conditional>
+            <param name="crossreference" value="model/crossreference.txt" />
+            <param name="logfile" value="true" />
+            <output name="log" file="model/log.txt" />
+            <output_collection name="models" type="list" count="1">
+                <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Creates protein complex model from HHsearch threading results.
+
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>
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