diff load_interpro.xml @ 0:532e76badbde draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/load_interpro.xml	Wed Aug 21 04:56:38 2019 -0400
@@ -0,0 +1,66 @@
+<?xml version="1.0"?>
+<tool id="load_interpro" name="Chado load InterProScan results" version="@WRAPPER_VERSION@.0">
+ <description>interpro</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <code file="chado.py"/>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+@START_PSQL@ &&
+
+chakin load interpro
+'$analysis_id'
+'$organism_id'
+'$input'
+
+$parse_go
+
+--query_type '$query_type'
+
+$match_on_name
+
+#if $re_name:
+  --re_name '$re_name'
+#end if
+
+$skip_missing
+
+| jq -S . > $results
+
+@ZIP_PSQL@
+    ]]></command>
+    <inputs>
+        <expand macro="psql_target"/>
+        <!-- arguments -->
+        <param name="input" label="InterProScan results" argument="input" type="data" format="xml" help="Path to the InterProScan XML file to load" />
+        <param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" />
+        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
+
+        <!-- options -->
+        <param name="query_type" label="Query type" argument="--query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />
+
+        <param name="match_on_name" label="Match On Name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
+
+        <param name="parse_go" label="Parse Go" argument="parse_go" type="boolean" truevalue="--parse_go" falsevalue="" help="Load GO annotation to the database" />
+
+        <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
+            <expand macro="sanitized"/>
+        </param>
+
+        <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features instead of aborting everything." />
+
+        <expand macro="wait_for"/>
+    </inputs>
+    <outputs>
+        <data format="json" name="results"/>
+        <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
+            <filter>psql_target['method'] == "pgtools"</filter>
+        </data>
+    </outputs>
+    <help>
+Load an InterProScan analysis, in the same way as does the tripal_analysis_intepro module
+
+@HELP@
+    </help>
+</tool>