diff macros.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/macros.xml	Wed Aug 21 04:56:38 2019 -0400
@@ -0,0 +1,134 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@LIB_VERSION@">python-chado</requirement>
+            <requirement type="package" version="1.5">jq</requirement>
+            <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
+            <requirement type="package" version="0.1">pglite</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@LIB_VERSION@">2.3.0</token>
+    <token name="@WRAPPER_VERSION@">@LIB_VERSION@</token>
+    <token name="@PG_VERSION@">11.2</token>
+
+    <xml name="stdio">
+        <stdio>
+            <regex level="fatal" match="Exception:" source="stderr" />
+            <regex level="fatal" match="error" source="stderr" />
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+        </citations>
+    </xml>
+
+    <token name="@HELP_OVERVIEW@"><![CDATA[
+        **Python-chado Overview**
+
+        Python-cado provides several tools allowing to load data into a remote Chado database.
+    ]]></token>
+
+    <token name="@HELP@"><![CDATA[
+    ]]></token>
+
+    <xml name="sanitized">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
+                <add source="(" target="\("/>
+                <add source=")" target="\)"/>
+            </mapping>
+        </sanitizer>
+    </xml>
+
+    <!-- I'm not proud of it, but it is needed for workflows -->
+    <xml name="wait_for">
+        <param name="wait_for"
+               type="data"
+               format="data"
+               optional="true"
+               label="Run this only after the following dataset is ready"
+               help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>
+    </xml>
+
+    <xml name="feature_rel">
+        <param name="rel_subject_re"
+               argument="--rel-subject-re"
+               type="text"
+               label="Regular expression to extract the unique name of the parent feature"
+               help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
+            <expand macro="sanitized"/>
+        </param>
+
+        <param name="rel_subject_type"
+               argument="--rel-subject-type"
+               type="text"
+               label="Sequence type of the parent"
+               help="this should be a Sequence Ontology term" />
+    </xml>
+
+    <xml name="psql_target">
+      <conditional name="psql_target">
+         <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables">
+              <option value="remote">Remote database</option>
+              <option value="pgtools">Database from history</option>
+          </param>
+          <when value="remote"/>
+          <when value="pgtools">
+            <param name="infile" type="data" format="postgresql" label="Input database" />
+            <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/>
+          </when>
+      </conditional>
+    </xml>
+
+    <token name="@START_PSQL@"><![CDATA[
+        #if $psql_target.method == 'pgtools'
+            tar -xjvf '$psql_target.infile' > /dev/null &&
+            . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
+        #else
+            if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
+              echo "__default: local" > '.auth.yml' &&
+              echo "local:" >> '.auth.yml' &&
+              echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
+              echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
+              echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
+              echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
+              echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
+              echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
+
+              export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
+            ; fi
+        #end if
+    ]]></token>
+
+    <token name="@STOP_PSQL@"><![CDATA[
+        #if $psql_target.method == 'pgtools'
+            &&
+            pglite stop -d ./postgresql &&
+            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
+            ;
+            ## Make sure psql is stopped even if loading script failed
+            pglite stop -d ./postgresql || true
+        #end if
+    ]]></token>
+
+    <token name="@ZIP_PSQL@"><![CDATA[
+        #if $psql_target.method == 'pgtools'
+            &&
+            pglite stop -d ./postgresql &&
+            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
+            tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
+            ;
+            ## Make sure psql is stopped even if loading script failed
+            pglite stop -d ./postgresql || true
+        #end if
+    ]]></token>
+</macros>