Mercurial > repos > iuc > mothur_mimarks_attributes

diff mimarks.attributes.xml @ 0:1a45cc9dc7ee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:30:43 -0400
parents
children 371a522fc3a1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mimarks.attributes.xml	Fri May 19 05:30:43 2017 -0400
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+<tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
+    <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$biosample_in" biosample_in.dat &&
+
+        echo 'mimarks.attributes(
+            xml=biosample_in.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
+        <!-- TODO: add package type options (currently none described in documentation apart from default)
+        <param name="package" type="select" label="package - select the mimarks package you would like to use">
+            <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
+        </param>-->
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="biosample_in" value="biosample.xml" ftype="xml"/>
+            <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command.
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1128/AEM.01541-09</citation>
+    </citations>
+</tool>