diff samples_qccheck.xml @ 2:de0af39266ef draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samples_qccheck.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,114 @@
+<tool id="samples_qccheck" name="RNASeq samples quality check" version="2.1.1">
+    <description>for transcript quantification</description>
+    <requirements>
+        <requirement type="package" version="2.1.1">trinity</requirement>
+        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
+        <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+        
+        ln -s "${matrix}" "input.matrix"
+        
+        &&
+        
+        PtR
+        --matrix "input.matrix"
+        
+        --samples "${samples}"
+        
+        --CPM --log2 --compare_replicates
+        
+        &&
+        
+        PtR
+        --matrix "input.matrix"
+        
+        --samples "${samples}"
+        
+        --CPM --log2 --sample_cor_matrix
+        
+        &&
+        
+        PtR
+        --matrix "input.matrix"
+        
+        --samples "${samples}"
+        
+        --CPM --log2 --prin_comp 3
+        
+        && mkdir out_pdf
+        && mv *rep_compare.pdf out_pdf/
+        && mv *sample_cor_matrix.pdf out_pdf/
+        && mv *principal_components.pdf out_pdf/
+        
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
+        <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
+    </inputs>
+    <outputs>
+        <collection name="reports" type="list" label="Quality check result files on ${on_string}">
+            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <output_collection name="reports">
+                <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
+                <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
+                <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
+                <element name="input.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf"/>
+                <element name="input.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool performs some Quality Checks on a RNASeq experiment, analysing the abundance estimation for different samples using a transcriptome assembled with Trinity.
+
+**Inputs**
+
+This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
+
+You must describe your samples and replicates with 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
+=========== ================
+
+The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
+
+**Output**
+
+This tool will produce several PDF files, see the following page for more information:
+
+.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+