diff organism_add_organism.xml @ 0:56390a41953e 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/organism_add_organism.xml	Mon Sep 11 05:53:37 2017 -0400
@@ -0,0 +1,127 @@
+<?xml version="1.0"?>
+<tool id="organism_add_organism" profile="16.04" name="Create an organism" version="@WRAPPER_VERSION@.0">
+    <description>in Tripal</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.5">jq</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+
+        @AUTH@
+
+        tripaille organism add_organism
+
+            #if str($species):
+                --species '$species'
+            #end if
+
+            #if str($description):
+                --comment '$description'
+            #end if
+
+            #if $infra.use_infra:
+                --infraspecific_rank '$infra.rank'
+                --infraspecific_name '$infra.name'
+            #end if
+
+            '$genus'
+            '$common'
+            '$abbr'
+
+            | jq -S . > $results
+    ]]></command>
+    <inputs>
+        <param name="genus"
+               type="text"
+               label="Genus"
+               help="e.g.: Homo" />
+
+        <param name="species"
+               argument="--species"
+               type="text"
+               label="Species"
+               optional="True"
+               help="e.g.: sapiens" />
+
+        <param name="abbr"
+               type="text"
+               label="Abbreviation"
+               help="e.g.: H. sapiens" />
+
+        <param name="common"
+               type="text"
+               label="Common name"
+               help="e.g.: Human" />
+
+        <param name="description"
+               argument="--comment"
+               type="text"
+               label="Description"
+               optional="True">
+            <expand macro="sanitized"/>
+        </param>
+
+        <conditional name="infra">
+            <param name="use_infra" type="boolean" checked="false" label="Specify an infraspecific rank" />
+            <when value="false"></when>
+            <when value="true">
+                <param name="rank"
+                       argument="--infraspecific_rank"
+                       type="select"
+                       label="Infraspecific Rank">
+                    <option value="subspecies">subspecies</option>
+                    <option value="varietas">varietas</option>
+                    <option value="subvariety">subvariety</option>
+                    <option value="forma">forma</option>
+                    <option value="subforma">subforma</option>
+                </param>
+                <param name="name"
+                       argument="--infraspecific_name"
+                       type="text"
+                       label="Infraspecific Name"
+                       help="The infraspecific name of the new organism (e.g. a strain name)" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="json" name="results" label="New Tripal organism" />
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="genus" value="Testus" />
+            <param name="species" value="testum" />
+            <param name="abbr" value="test" />
+            <param name="common" value="test stuff" />
+            <param name="common" value="My cool new test organism" />
+
+            <expand macro="test_result" />
+        </test>
+        <test expect_failure="true">
+            <param name="genus" value="Testus" />
+            <param name="species" value="testum" />
+            <param name="abbr" value="test" />
+            <param name="common" value="test stuff" />
+            <param name="common" value="My cool new test organism" />
+            <conditional name="infra">
+                <param name="use_infra" value="True" />
+                <param name="rank" value="subspecies" />
+                <param name="name" value="strain3" />
+            </conditional>
+
+            <expand macro="test_result" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        @HELP_OVERVIEW@
+
+        **Create Organism**
+
+        With this tool, you can create a new organism in the Tripal/Chado database
+
+        @HELP@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>