diff analysis_load_interpro.xml @ 0:dc0a6c9cea1c draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analysis_load_interpro.xml	Mon Sep 11 05:41:31 2017 -0400
@@ -0,0 +1,95 @@
+<?xml version="1.0"?>
+<tool id="analysis_load_interpro" profile="16.04" name="Load InterProScan results" version="@WRAPPER_VERSION@.0">
+    <description>into Tripal</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
+
+        &&
+
+        cp '${input}' "\${tmp_dir}/interpro.xml"
+
+        &&
+
+        @AUTH@
+
+        tripaille analysis load_interpro
+
+            @ANALYSIS@
+
+            --interpro_parameters '${params}'
+
+            ${parse_go}
+
+            @MATCHING@
+
+            "\${tmp_dir}/interpro.xml"
+
+        &&
+
+        echo "Data loaded" > $results
+    ]]></command>
+    <inputs>
+        <param name="input"
+               type="data"
+               format="xml"
+               label="InterProScan results" />
+
+        <param name="parse_go"
+               type="boolean"
+               checked="true"
+               truevalue="--parse_go"
+               falsevalue=""
+               label="Load GO annotation to the database" />
+
+        <param name="params"
+               type="text"
+               label="InterProScan parameters used to produce the results" />
+
+        <expand macro="matching"/>
+        <expand macro="analysis" />
+    </inputs>
+    <outputs>
+        <data format="txt" name="results" label="Load InterProScan results into Tripal" />
+    </outputs>
+    <tests>
+        <test expect_failure="true" expect_exit_code="1">
+            <param name="input" value="interpro.xml" />
+            <param name="parse_go" value="true" />
+            <param name="params" value="--some --param" />
+            <param name="query_type" value="mRNA" />
+            <param name="query_uniquename" value="true" />
+            <section name="analysis">
+                <param name="name" value="Some analysis" />
+                <param name="program" value="interproscan" />
+                <param name="program_version" value="58.2" />
+                <param name="algorithm" value="interproscan" />
+                <param name="source" value="NCBI" />
+                <param name="source_version" value="1.0" />
+                <param name="source_uri" value="http://ncbi.com/somewhere" />
+                <param name="description" value="My cool new test analysis" />
+                <param name="date" value="2016-12-12" />
+            </section>
+
+            <expand macro="test_result" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        @HELP_OVERVIEW@
+
+        **Load InterProScan results**
+
+        With this tool, you can load InterProScan results into the Tripal/Chado database.
+
+        A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source.
+
+        The `tripal_analysis_interpro <http://github.com/tripal/tripal_analysis_interpro>`_ module must be installed and configured on the Tripal instance.
+
+        @HELP@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>