diff macros.xml @ 0:030d63ede604 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 25 06:16:27 2019 -0500
@@ -0,0 +1,224 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.2">python-tripal</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex level="fatal" match="Exception:" source="stderr" />
+            <regex level="fatal" match="error" source="stderr" />
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">3.2</token>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1093/database/bat075</citation>
+        </citations>
+    </xml>
+
+    <token name="@HELP_OVERVIEW@"><![CDATA[
+        **Python-tripal Overview**
+
+        Python-tripal provides several tools allowing to load data into a remote Chado-based Tripal database.
+        The tripal_rest_api Tripal module must be installed on the remote server to use these tools.
+    ]]></token>
+
+    <token name="@HELP@"><![CDATA[
+        **Useful Links**
+
+        `Tripal project website <http://tripal.info/>`_
+
+        `Tripal REST API module <http://github.com/abretaud/tripal_rest_api>`_: a Tripal module required to use these galaxy tools
+    ]]></token>
+
+    <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>
+
+    <token name="@AUTH@"><![CDATA[
+        echo "__default: local" > '.auth.yml' &&
+        echo "local:" >> '.auth.yml' &&
+        echo "    tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
+        echo "    username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
+        echo "    password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&
+
+        TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
+    ]]></token>
+
+    <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="test_result">
+        <assert_stderr>
+            <has_text text="MissingSchema" />
+        </assert_stderr>
+    </xml>
+
+    <xml name="analysis">
+        <section name="analysis" title="Analysis" expanded="True">
+            <param name="name"
+                   type="text"
+                   label="The analysis name [mandatory]">
+                <expand macro="sanitized"/>
+            </param>
+
+            <param name="program"
+                   type="text"
+                   label="Program name [mandatory]"
+                   help="Name of the program that was used to perform this analysis">
+                <expand macro="sanitized"/>
+            </param>
+            <param name="program_version"
+                   type="text"
+                   label="Program version [mandatory]"
+                   help="Version of the program that was used to perform this analysis"/>
+            <param name="source"
+                   type="text"
+                   label="Source name [mandatory]"
+                   help="Where this analysis comes from">
+                <expand macro="sanitized"/>
+            </param>
+
+            <param name="source_version"
+                   argument="--sourceversion"
+                   type="text"
+                   optional="True"
+                   label="Source version" />
+            <param name="source_uri"
+                   argument="--sourceuri"
+                   type="text"
+                   optional="True"
+                   label="Source URI"
+                   help="URI where source data was retrieved" />
+            <param name="algorithm"
+                   argument="--algorithm"
+                   type="text"
+                   label="Algorithm"
+                   optional="True"
+                   help="Algorithm of the program that was used to perform this analysis" />
+            <param name="description"
+                   argument="--description"
+                   type="text"
+                   optional="True"
+                   label="Analysis description">
+                <expand macro="sanitized"/>
+            </param>
+            <param name="date"
+                   argument="--date_executed"
+                   type="text"
+                   optional="True"
+                   label="Execution date"
+                   help="Format: yyyy-mm-dd  Default: Today">
+                <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
+            </param>
+        </section>
+    </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="match_type">
+        <param name="match_type"
+               argument="--match-type"
+               type="select"
+               label="Match type for already loaded features">
+            <option value="uniquename" selected="true">Unique name</option>
+            <option value="name">Name</option>
+        </param>
+    </xml>
+
+    <xml name="matching">
+        <section name="matching" title="Feature matching" expanded="True">
+            <param name="query_type"
+                   type="text"
+                   label="The feature type of the blast query"
+                   help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
+
+            <param name="query_uniquename"
+                   type="boolean"
+                   checked="false"
+                   truevalue="--query_uniquename"
+                   falsevalue=""
+                   label="Find blast query features using their Unique name"
+                   help="Feature name will be used otherwise" />
+
+            <param name="query_re"
+                   type="text"
+                   optional="true"
+                   label="Regular expression to extract the feature name from the blast query name"
+                   help="leave empty if the first word in query name is sufficient">
+                <expand macro="sanitized"/>
+            </param>
+        </section>
+    </xml>
+
+    <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>
+
+    <token name="@MATCHING@"><![CDATA[
+        #if str($matching.query_re):
+            --query_re '${matching.query_re}'
+        #end if
+
+        $matching.query_uniquename
+
+        --query_type '$matching.query_type'
+    ]]></token>
+
+    <token name="@ANALYSIS@"><![CDATA[
+        #if $analysis.algorithm:
+            --algorithm '$analysis.algorithm'
+        #end if
+        #if $analysis.source_version:
+            --sourceversion '$analysis.source_version'
+        #end if
+        #if $analysis.source_uri:
+            --sourceuri '$analysis.source_uri'
+        #end if
+        #if $analysis.description:
+            --description '$analysis.description'
+        #end if
+        #if $analysis.date:
+            --date_executed '$analysis.date'
+        #end if
+
+        '$analysis.name'
+        '$analysis.program'
+        '$analysis.program_version'
+        '$analysis.source'
+    ]]></token>
+</macros>