diff contig_exn50_statistic.xml @ 0:1e8a2c87461a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/contig_exn50_statistic.xml	Thu Mar 23 10:18:11 2017 -0400
@@ -0,0 +1,44 @@
+<tool id="trinity_contig_exn50_statistic" name="Compute contig Ex90N50 statistic and Ex90 transcript count" version="@WRAPPER_VERSION@.0">
+    <description>from a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+
+    contig_ExN50_statistic.pl
+        '$matrix'
+        '$transcripts'
+        > '$output'
+
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="Matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
+        <param format="fasta" name="transcripts" type="data" label="Transcripts" help="De novo assembly of RNA-Seq data"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}: ExN50 statistics"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="count/contig_exn50_statistic/matrix.TMM.EXPR.matrix"/>
+            <param name="transcripts" value="count/contig_exn50_statistic/Trinity.fasta"/>
+            <output name="output" file="count/contig_exn50_statistic/ExN50.stats"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool computes the N50 statistic limited to the top most highly expressed transcripts that represent x% of the total normalized expression data. This requires that you have first performed transcript abundance estimation with 'Align reads and estimate abundance for a de novo assembly of RNA-Seq data by Trinity' tool and that you have built the expression matrix with 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool. 
+
+**Inputs**
+
+It takes as input a transcriptome assembled with Trinity and the matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>