diff describe_samples.xml @ 0:5bb8e7dcc404 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/describe_samples.xml	Fri Nov 18 06:07:54 2016 -0500
@@ -0,0 +1,68 @@
+<?xml version="1.0"?>
+<tool id="describe_samples" name="Describe samples" version="@WRAPPER_VERSION@.0">
+    <description>and replicates</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command detect_errors="aggressive"><![CDATA[
+        cp $sample_list $output
+      ]]></command>
+    <configfiles>
+        <configfile name="sample_list"><![CDATA[#for $sample in $samples:
+$sample.condition	$sample.name
+#end for]]></configfile>
+    </configfiles>
+    <inputs>
+        <repeat name="samples" title="Samples">
+            <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" optional="False" />
+            <param name="condition" type="text" label="Condition" help="e.g. ConditionA" optional="False" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="samples">
+                <param name="condition" value="ConditionA" />
+                <param name="name" value="CondA_replicate1" />
+            </repeat>
+            <repeat name="samples">
+                <param name="condition" value="ConditionA" />
+                <param name="name" value="CondA_replicate2" />
+            </repeat>
+            <repeat name="samples">
+                <param name="condition" value="ConditionB" />
+                <param name="name" value="CondB_replicate1" />
+            </repeat>
+            <repeat name="samples">
+                <param name="condition" value="ConditionB" />
+                <param name="name" value="CondB_replicate2" />
+            </repeat>
+            <output name="output" file="samples.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tools allows to describe your samples and replicates, producing a tabular file looking like this:
+
+        =========== ================
+        ConditionA  CondA_replicate1
+        ----------- ----------------
+        ConditionA  CondA_replicate2
+        ----------- ----------------
+        ConditionB  CondB_replicate1
+        ----------- ----------------
+        ConditionB  CondB_replicate2
+        ----------- ----------------
+        ConditionC  CondC_replicate1
+        ----------- ----------------
+        ConditionC  CondC_replicate2
+        ----------- ----------------
+        ConditionC  CondC_replicate3
+        =========== ================
+
+        IThe output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'.
+        The names in column 2 must match the names given to the datasets in your history.
+    ]]></help>
+    <expand macro="citation"/>
+</tool>