diff spring_map.xml @ 0:023800b21a2a draft

"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_map.xml	Tue Mar 23 13:54:20 2021 +0000
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+<tool id="spring_map" name="SPRING Map" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>with BLAST</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    spring_map.py
+        @pdb_source@
+        -l '$list'
+        -c '$cross'
+        -e $evalue
+        -o '$output'
+        -g '$log'
+    ]]>    </command>
+    <inputs>
+        <expand macro="pdb_source" />
+        <param name="list" type="data" format="tabular" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`." />
+        <param name="cross" type="data" format="tabular" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool." />
+        <param name="evalue" type="float" value="0.0" min="0.0" max="1.0" label="E-value Threshold" help="Specify an e-Value threshold to filter the alignment results" />
+        <expand macro="logfile" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="SPRING Map Cross Reference" />
+        <data format="txt" name="log" label="SPRING Map Log">
+            <filter>logfile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="pdb_source">
+                <param name="pdb_source_selector" value="history" />
+                <param name="ffdata" value="cross/pdb.ffdata" />
+                <param name="ffindex" value="cross/pdb.ffindex" />
+            </conditional>
+            <param name="list" value="map/chains.tabular" ftype="tabular" />
+            <param name="cross" value="cross/reference.tabular" ftype="tabular" />
+            <output name="output" file="map/mapped.reference.tabular" />
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="pdb_source">
+                <param name="pdb_source_selector" value="indexed" />
+                <param name="pdb" value="pdb01_cross" />
+            </conditional>
+            <param name="list" value="map/chains.tabular" ftype="tabular" />
+            <param name="cross" value="cross/reference.tabular" ftype="tabular" />
+            <param name="logfile" value="true" />
+            <output name="output" file="map/mapped.reference.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Creates additional columns for the SPRING cross reference containing the chain identifier of the homologues from the template library.
+
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>
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