diff obisort.xml @ 0:aca6a8c9cf83 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/obisort.xml	Wed Apr 12 17:38:00 2017 -0400
@@ -0,0 +1,67 @@
+<tool id="obi_sort" name="obisort" version="@WRAPPER_VERSION@">
+    <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command>
+
+        <![CDATA[
+            obisort
+            -k '$key'
+            ${reverse}
+            '$input' > '$output'
+        ]]>
+
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
+        <param name="key" type="text" label="key" />
+        <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
+        <param name="out_format" type="select" label="Output data type">
+            <option value="fasta">fasta</option>
+            <option value="fastq">fastq</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
+            <change_format>
+                <when input="out_format" value="fasta" format="fasta" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obiclean_advanced.fasta" />
+            <param name="key" value="count"/>
+            <param name="reverse" value="False"/>
+            <param name="out_format" value="fasta"/>
+            <output name="output" file="output_obisort.fasta" ftype="fasta"/>
+        </test>
+        <test>
+            <param name="input" value="output_obiclean_advanced.fasta" />
+            <param name="key" value="count"/>
+            <param name="reverse" value="True"/>
+            <param name="out_format" value="fastq"/>
+            <output name="output" file="output_obisort.fastq" ftype="fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
+
+@OBITOOLS_LINK@
+
+        ]]>
+
+    </help>
+    <expand macro="citation" />
+</tool>